Het-PDB Navi2 (PDB: 6FYY)

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Ligands
Code	Name	Link
GCP	Phosphomethylphosphonic acid guanylate ester	PoSSuM
MET	Methionine	PoSSuM
MG	Magnesium ion	PoSSuM
ZN	Zinc ion	PoSSuM

Non-standard Residues
Code	Name	Show
1MA	6-hydro-1-methyladenosine-5'-monophosphate
1MG	1n-methylguanosine-5'-monophosphate
2MG	2n-methylguanosine-5'-monophosphate
5MC	5-methylcytidine-5'-monophosphate
7MG	7n-methyl-8-hydroguanosine-5'-monophosphate
AYA	N-acetylalanine
C4J	(5s)-5-{3-[(3s)-3-amino-3-carboxypropyl]-1-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl}-2,5-anhydro-1-O-phosphono-L-arabinitol
H2U	5,6-dihydrouridine-5'-monophosphate
M2G	N2-dimethylguanosine-5'-monophosphate
MA6	6n-dimethyladenosine-5'-monophoshate
PSU	Pseudouridine-5'-monophosphate
RIA	2'-O-[(5'-phospho)ribosyl]adenosine-5'-monophosphate
T6A	N-[N-(9-B-D-ribofuranosylpurin-6-yl)carbamoyl]threonine-5'-monophosphate

Glycosylation
Code	Name	Emphasize

Modification
Code	Name	Show

Download interaction data: 6FYY

Code :

6FYY PDBj RCSB PDB PDBe

Header :

RIBOSOME

Title :

Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (model C2)

Release Data :

2018-12-05

Compound :

mol_id	molecule	chains
1	tRNAi	1

mol_id	molecule	chains
2	18S ribosomal RNA	2

mol_id	molecule	chains
3	mRNA (31-MER)	3

mol_id	molecule	chains
4	40S ribosomal protein S0	A

mol_id	molecule	chains
5	40S ribosomal protein S1	B

mol_id	molecule	chains
6	KLLA0F09812p	C

mol_id	molecule	chains
7	KLLA0D08305p	D

mol_id	molecule	chains
8	40S ribosomal protein S4	E

mol_id	molecule	chains
9	KLLA0D10659p	F

mol_id	molecule	chains
10	40S ribosomal protein S6	G

mol_id	molecule	chains
11	40S ribosomal protein S7	H

mol_id	molecule	chains
12	40S ribosomal protein S8	I

mol_id	molecule	chains
13	KLLA0E23673p	J

mol_id	molecule	chains
14	KLLA0B08173p	K

mol_id	molecule	chains
15	KLLA0A10483p	L

mol_id	molecule	chains
16	40S ribosomal protein S12	M

mol_id	molecule	chains
17	KLLA0F18040p	N

mol_id	molecule	chains	synonym
18	40S ribosomal protein S14	O	RP59

mol_id	molecule	chains
19	KLLA0F07843p	P

mol_id	molecule	chains
20	40S ribosomal protein S16	Q

mol_id	molecule	chains
21	KLLA0B01474p	R

mol_id	molecule	chains
22	KLLA0B01562p	S

mol_id	molecule	chains
23	KLLA0A07194p	T

mol_id	molecule	chains
24	KLLA0F25542p	U

mol_id	molecule	chains
25	40S ribosomal protein S21	V

mol_id	molecule	chains
26	40S ribosomal protein S22	W

mol_id	molecule	chains
27	KLLA0B11231p	X

mol_id	molecule	chains
28	40S ribosomal protein S24	Y

mol_id	molecule	chains
29	KLLA0B06182p	Z

mol_id	molecule	chains
30	40S ribosomal protein S26	a

mol_id	molecule	chains
31	40S ribosomal protein S27	b

mol_id	molecule	chains	synonym
32	40S ribosomal protein S28	c	S33

mol_id	molecule	chains
33	40S ribosomal protein S29	d

mol_id	molecule	chains
34	40S ribosomal protein S30	e

mol_id	molecule	chains
35	Ubiquitin-40S ribosomal protein S27a	f

mol_id	molecule	chains
36	KLLA0E12277p	g

mol_id	molecule	chains	synonym
37	60S ribosomal protein L41-A	h	L47,Large ribosomal subunit protein eL41-A,YL41

mol_id	molecule	chains	synonym
38	Eukaryotic translation initiation factor 1A	i	eIF-1A,Eukaryotic translation initiation factor 4C,eIF-4C

mol_id	molecule	chains	synonym
39	Eukaryotic translation initiation factor 2 subunit alpha	j	eIF-2-alpha

mol_id	molecule	chains	synonym
40	Eukaryotic translation initiation factor 2 subunit gamma	k	eIF-2-gamma

mol_id	molecule	chains	synonym
41	Eukaryotic translation initiation factor 2 subunit beta	l	eIF-2-beta

mol_id	molecule	chains	synonym
42	Eukaryotic translation initiation factor 5	m	eIF-5

mol_id	molecule	chains	synonym
43	Eukaryotic translation initiation factor 3 subunit A	o	eIF3a,Eukaryotic translation initiation factor 3 110 kDa subunit homolog,eIF3 p110,Translation initiation factor eIF3,p110 subunit homolog

mol_id	molecule	chains	synonym
44	Eukaryotic translation initiation factor 3 subunit B	p	eIF3b,Cell cycle regulation and translation initiation protein,Eukaryotic translation initiation factor 3 90 kDa subunit,eIF3 p90,Translation initiation factor eIF3 p90 subunit

mol_id	molecule	chains	synonym
45	eIF3c,Eukaryotic translation initiation factor 3 subunit C	q	eIF3c,Eukaryotic translation initiation factor 3 93 kDa subunit,eIF3 p93,Nuclear transport protein NIP1,Translation initiation factor eIF3,p93 subunit

mol_id	molecule	chains	synonym
46	Eukaryotic translation initiation factor 3 subunit G	r	eIF3g,Eukaryotic translation initiation factor 3 RNA-binding subunit,eIF-3 RNA-binding subunit,Translation initiation factor eIF3 p33 subunit homolog,eIF3 p33 homolog

mol_id	molecule	chains	synonym
47	Eukaryotic translation initiation factor 3 subunit I	s	eIF3i,Eukaryotic translation initiation factor 3 39 kDa subunit homolog,eIF-3 39 kDa subunit homolog

Source :

mol_id	organism_scientific
1	Saccharomyces cerevisiae (taxid:4932)

mol_id	organism_scientific
2	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid:284590)

mol_id	organism_scientific
3	Saccharomyces cerevisiae (taxid:4932)
	synthetic: yes

mol_id	organism_scientific	organism_common
4	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid:284590)	Yeast

mol_id	organism_scientific	organism_common
5	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid:284590)	Yeast

mol_id	organism_scientific	organism_common
6	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid:284590)	Yeast

mol_id	organism_scientific	organism_common
7	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid:284590)	Yeast

mol_id	organism_scientific	organism_common
8	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid:284590)	Yeast

mol_id	organism_scientific	organism_common
9	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid:284590)	Yeast

mol_id	organism_scientific	organism_common
10	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid:284590)	Yeast

mol_id	organism_scientific	organism_common
11	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid:284590)	Yeast

mol_id	organism_scientific	organism_common
12	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid:284590)	Yeast

mol_id	organism_scientific	organism_common
13	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid:284590)	Yeast

mol_id	organism_scientific	organism_common
14	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid:284590)	Yeast

mol_id	organism_scientific	organism_common
15	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid:284590)	Yeast

mol_id	organism_scientific	organism_common
16	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid:284590)	Yeast

mol_id	organism_scientific	organism_common
17	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid:284590)	Yeast

mol_id	organism_scientific	organism_common
18	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid:284590)	Yeast

mol_id	organism_scientific	organism_common
19	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid:284590)	Yeast

mol_id	organism_scientific	organism_common
20	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid:284590)	Yeast

mol_id	organism_scientific	organism_common
21	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid:284590)	Yeast

mol_id	organism_scientific	organism_common
22	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid:284590)	Yeast

mol_id	organism_scientific	organism_common
23	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid:284590)	Yeast

mol_id	organism_scientific	organism_common
24	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid:284590)	Yeast

mol_id	organism_scientific	organism_common
25	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid:284590)	Yeast

mol_id	organism_scientific	organism_common
26	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid:284590)	Yeast

mol_id	organism_scientific	organism_common
27	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid:284590)	Yeast

mol_id	organism_scientific	organism_common
28	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid:284590)	Yeast

mol_id	organism_scientific	organism_common
29	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid:284590)	Yeast

mol_id	organism_scientific	organism_common
30	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid:284590)	Yeast

mol_id	organism_scientific	organism_common
31	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid:284590)	Yeast

mol_id	organism_scientific	organism_common
32	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid:284590)	Yeast

mol_id	organism_scientific	organism_common
33	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid:284590)	Yeast

mol_id	organism_scientific	organism_common
34	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid:284590)	Yeast

mol_id	organism_scientific	organism_common
35	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid:284590)	Yeast

mol_id	organism_scientific	organism_common
36	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid:284590)	Yeast

mol_id	organism_scientific	organism_common
37	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid:284590)	Yeast

mol_id	organism_scientific	organism_common	expression_system
38	Saccharomyces cerevisiae (taxid:4932)	Baker's yeast	Escherichia coli BL21(DE3) (taxid:469008)
	gene: TIF11, YMR260C, YM8156.02C

mol_id	organism_scientific	organism_common	expression_system
39	Saccharomyces cerevisiae (taxid:4932)	Baker's yeast	Saccharomyces cerevisiae (taxid:4932)
	gene: SUI2, TIF211, YJR007W, J1429

mol_id	organism_scientific	organism_common	expression_system
40	Saccharomyces cerevisiae (taxid:4932)	Baker's yeast	Saccharomyces cerevisiae (taxid:4932)
	gene: GCD11, TIF213, YER025W

mol_id	organism_scientific	organism_common	expression_system
41	Saccharomyces cerevisiae (taxid:4932)	Baker's yeast	Saccharomyces cerevisiae (taxid:4932)
	gene: SUI3, TIF212, YPL237W

mol_id	organism_scientific	organism_common	expression_system
42	Saccharomyces cerevisiae (taxid:4932)	Baker's yeast	Escherichia coli BL21(DE3) (taxid:469008)
	gene: TIF5, YPR041W, YP3085.05

mol_id	organism_scientific	organism_common	expression_system
43	Saccharomyces cerevisiae (taxid:4932)	Baker's yeast	Saccharomyces cerevisiae (taxid:4932)
	gene: RPG1, TIF32, YBR079C, YBR0734

mol_id	organism_scientific	organism_common	expression_system
44	Saccharomyces cerevisiae (taxid:4932)	Baker's yeast	Saccharomyces cerevisiae (taxid:4932)
	gene: PRT1, CDC63, YOR361C

mol_id	organism_scientific	organism_common	expression_system
45	Saccharomyces cerevisiae (taxid:4932)	Baker's yeast	Saccharomyces cerevisiae (taxid:4932)
	gene: NIP1, YMR309C, YM9924.01C, YM9952.11C

mol_id	organism_scientific	organism_common	expression_system
46	Saccharomyces cerevisiae (taxid:4932)	Baker's yeast	Saccharomyces cerevisiae (taxid:4932)
	gene: TIF35, SCY_1313

mol_id	organism_scientific	organism_common	expression_system
47	Saccharomyces cerevisiae (taxid:4932)	Baker's yeast	Saccharomyces cerevisiae (taxid:4932)
	gene: TIF34, SCY_4321

Authors :

Llacer, J.L., Hussain, T., Gordiyenko, Y., Ramakrishnan, V.

Keywords :

ribosome, translation, initiation factors, 40S, eIF1A, eIF3, eIF2, eIF5, tRNAi, 48S PIC, small ribosome subunit

Exp. method :

ELECTRON MICROSCOPY ( 3.02 Å )

Citation :

Translational initiation factor eIF5 replaces eIF1 on the 40S ribosomal subunit to promote start-codon recognition.

Llacer, J.L.,Hussain, T.,Saini, A.K. et al.
(2018) Elife 7

PubMed: 30475211
DOI: 10.7554/eLife.39273

Chain :	A
UniProt :	Q6CN12 (RSSA_KLULA)
Reaction :	-

Chain :	B
UniProt :	Q6CWD0 (RS3A_KLULA)
Reaction :	-

Chain :	C
UniProt :	Q6CKL3 (Q6CKL3_KLULA)
Reaction :	-

Chain :	D
UniProt :	Q6CRK7 (Q6CRK7_KLULA)
Reaction :	-

Chain :	E
UniProt :	Q6CWJ2 (Q6CWJ2_KLULA)
Reaction :	-

Chain :	F
UniProt :	Q6CRA3 (Q6CRA3_KLULA)
Reaction :	-

Chain :	G
UniProt :	Q6CM04 (RS6_KLULA)
Reaction :	-

Chain :	H
UniProt :	Q6CTD6 (Q6CTD6_KLULA)
Reaction :	-

Chain :	I
UniProt :	Q6CMG3 (Q6CMG3_KLULA)
Reaction :	-

Chain :	J
UniProt :	Q6CM18 (Q6CM18_KLULA)
Reaction :	-

Chain :	K
UniProt :	Q6CVZ5 (Q6CVZ5_KLULA)
Reaction :	-

Chain :	L
UniProt :	Q6CX80 (Q6CX80_KLULA)
Reaction :	-

Chain :	M
UniProt :	Q6CLU4 (Q6CLU4_KLULA)
Reaction :	-

Chain :	N
UniProt :	Q6CJK0 (Q6CJK0_KLULA)
Reaction :	-

Chain :	O
UniProt :	P27069 (RS14_KLULA)
Reaction :	-

Chain :	P
UniProt :	Q6CKV4 (Q6CKV4_KLULA)
Reaction :	-

Chain :	Q
UniProt :	Q875N2 (RS16_KLULA)
Reaction :	-

Chain :	R
UniProt :	Q6CWU3 (Q6CWU3_KLULA)
Reaction :	-

Chain :	S
UniProt :	Q6CWT9 (Q6CWT9_KLULA)
Reaction :	-

Chain :	T
UniProt :	Q6CXM0 (Q6CXM0_KLULA)
Reaction :	-

Chain :	U
UniProt :	Q6CIM1 (Q6CIM1_KLULA)
Reaction :	-

Chain :	V
UniProt :	Q6CXT6 (RS21_KLULA)
Reaction :	-

Chain :	W
UniProt :	Q6CW21 (RS22_KLULA)
Reaction :	-

Chain :	X
UniProt :	F2Z602 (F2Z602_KLULA)
Reaction :	-

Chain :	Y
UniProt :	Q6CU44 (Q6CU44_KLULA)
Reaction :	-

Chain :	Z
UniProt :	Q6CW78 (Q6CW78_KLULA)
Reaction :	-

Chain :	a
UniProt :	Q6CS01 (Q6CS01_KLULA)
Reaction :	-

Chain :	b
UniProt :	Q6CNL2 (Q6CNL2_KLULA)
Reaction :	-

Chain :	c
UniProt :	P33285 (RS28_KLULA)
Reaction :	-

Chain :	d
UniProt :	Q6CPG3 (RS29_KLULA)
Reaction :	-

Chain :	e
UniProt :	Q6CUH5 (Q6CUH5_KLULA)
Reaction :	-

Chain :	f
UniProt :	P69061 (RS27A_KLULA)
Reaction :	-

Chain :	g
UniProt :	Q6CNI7 (Q6CNI7_KLULA)
Reaction :	-

Chain :	h
UniProt :	P0CX86 (RS32A_YEAST)
Reaction :	-

Chain :	i
UniProt :	P38912 (IF1A_YEAST)
Reaction :	-

Chain :	j
UniProt :	P20459 (IF2A_YEAST)
Reaction :	-

Chain :

UniProt :

P32481 (IF2G_YEAST)

Reaction:	EC:	Evidence:
Reaction:	Physiological Direction:	Evidence:
GTP + H2O = GDP + H(+) + phosphate	3.6.5.3	PubMed:3888990
GTP + H2O = GDP + H(+) + phosphate	-	PubMed:3888990

Chain :	l
UniProt :	P09064 (IF2B_YEAST)
Reaction :	-

Chain :	m
UniProt :	P38431 (IF5_YEAST)
Reaction :	-

Chain :	o
UniProt :	P38249 (EIF3A_YEAST)
Reaction :	-

Chain :	p
UniProt :	P06103 (EIF3B_YEAST)
Reaction :	-

Chain :	q
UniProt :	P32497 (EIF3C_YEAST)
Reaction :	-

Chain :	r
UniProt :	A6ZZ25 (EIF3G_YEAS7)
Reaction :	-

Chain :	s
UniProt :	A6ZMK5 (EIF3I_YEAS7)
Reaction :	-

PDB ID: 6FYY

Hetero Atom Contents

Structure summary

Reaction