Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 36-mer - A1BCDEFGHIJKLMNOPQRSTUVWXYZabcdefghij 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 1208.67 kDa 
• Atom Count: 77850 
• Residue Count: 6836 
• Unique protein chains: 36
• Unique nucleic acid chains: 1

3JAM

CryoEM structure of 40S-eIF1A-eIF1 complex from yeast

• DOI: 10.2210/pdb3JAM/pdb
• EMDataResource: EMD-3047

• Classification: TRANSLATION
• Organism(s): Kluyveromyces lactis, Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2015-06-17 Released: 2015-08-12 
• Deposition Author(s): Llacer, J.L., Hussain, T., Ramakrishnan, V.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.46 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Conformational Differences between Open and Closed States of the Eukaryotic Translation Initiation Complex.

Llacer, J.L., Hussain, T., Marler, L., Aitken, C.E., Thakur, A., Lorsch, J.R., Hinnebusch, A.G., Ramakrishnan, V.

(2015) Mol Cell 59: 399-412

• PubMed: 26212456 
• DOI: 10.1016/j.molcel.2015.06.033
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Translation initiation in eukaryotes begins with the formation of a pre-initiation complex (PIC) containing the 40S ribosomal subunit, eIF1, eIF1A, eIF3, ternary complex (eIF2-GTP-Met-tRNAi), and eIF5. The PIC, in an open conformation, attaches to the 5' end of the mRNA and scans to locate the start codon, whereupon it closes to arrest scanning. We present single particle cryo-electron microscopy (cryo-EM) reconstructions of 48S PICs from yeast in these open and closed states, at 6.0 Å and 4.9 Å, respectively. These reconstructions show eIF2β as well as a configuration of eIF3 that appears to encircle the 40S, occupying part of the subunit interface. Comparison of the complexes reveals a large conformational change in the 40S head from an open mRNA latch conformation to a closed one that constricts the mRNA entry channel and narrows the P site to enclose tRNAi, thus elucidating key events in start codon recognition.

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Organizational Affiliation: 

MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK. Electronic address: [e-mail].

Macromolecules

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
uS5	C	259	Kluyveromyces lactis	Mutation(s): 0
Find proteins for Q6CKL3 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore Q6CKL3  Go to UniProtKB:  Q6CKL3

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
uS3	D	237	Kluyveromyces lactis	Mutation(s): 0
Find proteins for Q6CRK7 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore Q6CRK7  Go to UniProtKB:  Q6CRK7

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details
uS7	F	227	Kluyveromyces lactis	Mutation(s): 0
Find proteins for Q6CRA3 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore Q6CRA3  Go to UniProtKB:  Q6CRA3

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details
eS6	G	236	Kluyveromyces lactis	Mutation(s): 0
Find proteins for Q6CM04 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore Q6CM04  Go to UniProtKB:  Q6CM04

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details
eS7	H	190	Kluyveromyces lactis	Mutation(s): 0
Find proteins for Q6CTD6 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore Q6CTD6  Go to UniProtKB:  Q6CTD6

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details
uS4	J	188	Kluyveromyces lactis	Mutation(s): 0
Find proteins for Q6CM18 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore Q6CM18  Go to UniProtKB:  Q6CM18

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details
eS12	M	134	Kluyveromyces lactis	Mutation(s): 0
Find proteins for Q6CLU4 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore Q6CLU4  Go to UniProtKB:  Q6CLU4

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details
uS15	N	151	Kluyveromyces lactis	Mutation(s): 0
Find proteins for Q6CJK0 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore Q6CJK0  Go to UniProtKB:  Q6CJK0

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details
uS11	O	137	Kluyveromyces lactis	Mutation(s): 0
Find proteins for P27069 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore P27069  Go to UniProtKB:  P27069

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details
uS9	Q	143	Kluyveromyces lactis	Mutation(s): 0
Find proteins for Q875N2 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore Q875N2  Go to UniProtKB:  Q875N2

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details
eS17	R	136	Kluyveromyces lactis	Mutation(s): 0
Find proteins for Q6CWU3 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore Q6CWU3  Go to UniProtKB:  Q6CWU3

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details
eS19	T	144	Kluyveromyces lactis	Mutation(s): 0
Find proteins for Q6CXM0 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore Q6CXM0  Go to UniProtKB:  Q6CXM0

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details
uS8	W	130	Kluyveromyces lactis	Mutation(s): 0
Find proteins for Q6CW21 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore Q6CW21  Go to UniProtKB:  Q6CW21

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details
uS12	X	145	Kluyveromyces lactis	Mutation(s): 0
Find proteins for F2Z602 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore F2Z602  Go to UniProtKB:  F2Z602

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details
eS25	Z	108	Kluyveromyces lactis	Mutation(s): 0
Find proteins for Q6CW78 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore Q6CW78  Go to UniProtKB:  Q6CW78

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details
eS26	a	119	Kluyveromyces lactis	Mutation(s): 0
Find proteins for Q6CS01 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore Q6CS01  Go to UniProtKB:  Q6CS01

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details
eS27	b	82	Kluyveromyces lactis	Mutation(s): 0
Find proteins for Q6CNL2 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore Q6CNL2  Go to UniProtKB:  Q6CNL2

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details
uS14	d	56	Kluyveromyces lactis	Mutation(s): 0
Find proteins for Q6CPG3 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore Q6CPG3  Go to UniProtKB:  Q6CPG3

Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details
eS31	f	150	Kluyveromyces lactis	Mutation(s): 0
Find proteins for P69061 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore P69061  Go to UniProtKB:  P69061

Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details
eL41	h	25	Kluyveromyces lactis	Mutation(s): 0
Find proteins for P0CX86 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX86  Go to UniProtKB:  P0CX86

Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details
eIF1A	i	153	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P38912 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38912  Go to UniProtKB:  P38912

Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details
eIF1	j	108	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P32911 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32911  Go to UniProtKB:  P32911

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details
eS8	I	201	Kluyveromyces lactis	Mutation(s): 0
Find proteins for Q6CMG3 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore Q6CMG3  Go to UniProtKB:  Q6CMG3

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details
eS10	K	106	Kluyveromyces lactis	Mutation(s): 0
Find proteins for Q6CVZ5 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore Q6CVZ5  Go to UniProtKB:  Q6CVZ5

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details
uS17	L	156	Kluyveromyces lactis	Mutation(s): 0
Find proteins for Q6CX80 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore Q6CX80  Go to UniProtKB:  Q6CX80

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details
uS19	P	142	Kluyveromyces lactis	Mutation(s): 0
Find proteins for Q6CKV4 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore Q6CKV4  Go to UniProtKB:  Q6CKV4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
uS2	A	254	Kluyveromyces lactis	Mutation(s): 0
Find proteins for Q6CN12 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore Q6CN12  Go to UniProtKB:  Q6CN12

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details
uS13	S	146	Kluyveromyces lactis	Mutation(s): 0
Find proteins for Q6CWT9 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore Q6CWT9  Go to UniProtKB:  Q6CWT9

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details
uS10	U	117	Kluyveromyces lactis	Mutation(s): 0
Find proteins for Q6CIM1 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore Q6CIM1  Go to UniProtKB:  Q6CIM1

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details
eS21	V	87	Kluyveromyces lactis	Mutation(s): 0
Find proteins for Q6CXT6 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore Q6CXT6  Go to UniProtKB:  Q6CXT6

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details
eS24	Y	135	Kluyveromyces lactis	Mutation(s): 0
Find proteins for Q6CU44 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore Q6CU44  Go to UniProtKB:  Q6CU44

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
eS1	B	255	Kluyveromyces lactis	Mutation(s): 0
Find proteins for Q6CWD0 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore Q6CWD0  Go to UniProtKB:  Q6CWD0

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details
eS28	c	67	Kluyveromyces lactis	Mutation(s): 0
Find proteins for P33285 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore P33285  Go to UniProtKB:  P33285

Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details
eS30	e	63	Kluyveromyces lactis	Mutation(s): 0
Find proteins for Q6CUH5 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore Q6CUH5  Go to UniProtKB:  Q6CUH5

Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details
RACK1	g	326	Kluyveromyces lactis	Mutation(s): 0
Find proteins for Q6CNI7 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore Q6CNI7  Go to UniProtKB:  Q6CNI7

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details
eS4	E	261	Kluyveromyces lactis	Mutation(s): 0
Find proteins for Q6CWJ2 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore Q6CWJ2  Go to UniProtKB:  Q6CWJ2

Entity ID: 1
Molecule	Chains	Length	Organism
18S rRNA	2	1799	Kluyveromyces lactis

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	a, b, f	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	2, J, f	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.46 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-06-17 
• Released Date: 2015-08-12 
Deposition Author(s): Llacer, J.L., Hussain, T., Ramakrishnan, V.

Revision History 

• Version 1.0: 2015-08-12
  Type: Initial release
  
• Version 1.1: 2015-09-02
  Changes: Database references
• Version 1.2: 2018-07-18
  Changes: Data collection