OCA Atlas for 3JAM

3JAM

Translation

date

Jun 17, 2015

title

Cryoem Structure Of 40s-Eif1a-Eif1 Complex From Yeast

authors

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

compound

source

Molecule: 18s Rrna
Chain: 2

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Us2
Chain: A

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es1
Chain: B

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Us5
Chain: C

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Us3
Chain: D

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es4
Chain: E

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Us7
Chain: F

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es6
Chain: G

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es7
Chain: H

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es8
Chain: I

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Us4
Chain: J

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es10
Chain: K

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Us17
Chain: L

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es12
Chain: M

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Us15
Chain: N

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Us11
Chain: O

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Us19
Chain: P

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Us9
Chain: Q

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es17
Chain: R

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Us13
Chain: S

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es19
Chain: T

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Us10
Chain: U

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es21
Chain: V

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Us8
Chain: W

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Us12
Chain: X

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es24
Chain: Y

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es25
Chain: Z

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es26
Chain: a

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es27
Chain: b

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es28
Chain: c

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Us14
Chain: d

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es30
Chain: e

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Es31
Chain: f

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Rack1
Chain: g

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: El41
Chain: h

Organism_scientific: Kluyveromyces Lactis
Organism_taxid: 28985

Molecule: Eif1a
Chain: I
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Rosetta
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ptyb2

Molecule: Eif1
Chain: j
Engineered: Yes

symmetry

Space Group: P 1

R_factor

R_Free

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
1.000	1.000	1.000	90.00	90.00	90.00

method

Electron Microscopy

resolution

3.46 Å

ligand

MG, ZN

enzyme

Gene
Ontology

Chain	Function	Process	Component
A
B
C
D
E
F
G
H
I
J
K, Z
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
a
b
c
d
e
f
g	GDP-dissociation inhibitor a...
h
i
j

Primary reference

Conformational Differences between Open and Closed States of the Eukaryotic Translation Initiation Complex., Llacer JL, Hussain T, Marler L, Aitken CE, Thakur A, Lorsch JR, Hinnebusch AG, Ramakrishnan V, Mol Cell. 2015 Aug 6;59(3):399-412. doi: 10.1016/j.molcel.2015.06.033. Epub 2015 , Jul 23. PMID:26212456

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1527 Kb) [Save to disk]

Biological Unit Coordinates (3jam.pdb1.gz) 1516 Kb

LPC: Ligand-Protein Contacts for 3JAM

CSU: Contacts of Structural Units for 3JAM

Retrieve 3JAM in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 3JAM from S2C, [Save to disk]

View 3JAM in 3D

Proteopedia, because life has more than 2D.

On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.

On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 3JAM

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3jam_C] [3jam_V] [3jam_G] [3jam_e] [3jam_2] [3jam_I] [3jam_c] [3jam_O] [3jam_b] [3jam_g] [3jam_Z] [3jam_i] [3jam_Q] [3jam_T] [3jam_B] [3jam_U] [3jam_R] [3jam_a] [3jam_h] [3jam_f] [3jam_J] [3jam_L] [3jam_K] [3jam_F] [3jam] [3jam_P] [3jam_N] [3jam_X] [3jam_D] [3jam_M] [3jam_S] [3jam_d] [3jam_H] [3jam_j] [3jam_W] [3jam_Y] [3jam_E] [3jam_A]

SWISS-PROT database:

Domain organization of by SWISSPFAM

Domains found in 3JAM: [KH] [KOW] [Ribosomal_S10] [Ribosomal_S13_N] [Ribosomal_S15] [Ribosomal_S19e] [Ribosomal_S27] [Ribosomal_S3Ae] [Ribosomal_S4] [Ribosomal_S6e] [S4] [UBQ] [WD40] [eIF1a ] by SMART

Other resources with information on 3JAM

Community annotation for 3JAM at PDBWiki (http://pdbwiki.org)

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]