5M80 | pdb_00005m80

Translation initiation factor 4E in complex with (RP)-iPr-m7GppSpG mRNA 5' cap analog

PDB DOI: https://doi.org/10.2210/pdb5M80/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-10-28 Released: 2017-12-20
Deposition Author(s): Warminski, M., Nowak, E., Kowalska, J., Jemielity, J., Nowotny, M.
Funding Organization(s): Ministry of Science and Higher Education

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free:
0.258 (Depositor), 0.260 (DCC)
R-Value Work:
0.204 (Depositor), 0.206 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Translation initiation factor 4E in complex with (RP)-iPr-m7GppSpG mRNA 5' cap analog

Warminski, M., Nowak, E., Kubacka, D., Kowalska, J., Nowotny, M., Jemielity, J.

To be published.

Macromolecule Content

Total Structure Weight: 90.48 kDa
Atom Count: 5,690
Modeled Residue Count: 683
Deposited Residue Count: 760
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 4E	A, B [auth C], C [auth B], D	190	Mus musculus	Mutation(s): 0 Gene Names: Eif4e
UniProt & NIH Common Fund Data Resources
Find proteins for P63073 (Mus musculus) Explore P63073 Go to UniProtKB: P63073
IMPC: MGI:95305
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63073
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7L2 Query on 7L2 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B]	E [auth A], G [auth B]	[[[(3~{a}~{R},4~{R},6~{R},6~{a}~{R})-4-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-7-ium-9-yl)-2,2-dimethyl-3~{a},4,6,6~{a}-tetrahydrofuro[3,4-d][1,3]dioxol-6-yl]methoxy-oxidanyl-phosphoryl]oxy-sulfanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate C₂₄ H₃₄ N₁₀ O₁₇ P₃ S DSKLYZYSTSOTOM-RGGYBXOHSA-O		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B]	F [auth A], H [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Interactions & Density Focus chain F [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free: 0.258 (Depositor), 0.260 (DCC)
R-Value Work: 0.204 (Depositor), 0.206 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.237	α = 87.53
b = 38.271	β = 95.37
c = 146.818	γ = 102.94

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-12-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Higher Education	Poland	DI2012 024842

Revision History (Full details and data files)

Version 1.0: 2017-12-20
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description

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