8AMR | pdb_00008amr

Coiled-coil domain of human TRIM3

PDB DOI: https://doi.org/10.2210/pdb8AMR/pdb

Classification: ANTIVIRAL PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-08-04 Released: 2023-11-15
Deposition Author(s): Perez-Borrajero, C., Murciano, B., Hennig, J.
Funding Organization(s): EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND, German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.80 Å
R-Value Free:
0.321 (Depositor), 0.330 (DCC)
R-Value Work:
0.273 (Depositor), 0.273 (DCC)
R-Value Observed:
0.275 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 8AMR

This is version 1.2 of the entry. See complete history.

Literature

Structural and biophysical studies of TRIM2 and TRIM3

Perez-Borrajero, C., Hennig, J.

To be published.

Macromolecule Content

Total Structure Weight: 105.26 kDa
Atom Count: 3,265
Modeled Residue Count: 456
Deposited Residue Count: 957
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tripartite motif-containing protein 3	A, B, C	319	Homo sapiens	Mutation(s): 0 Gene Names: TRIM3, BERP, RNF22, RNF97 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for O75382 (Homo sapiens) Explore O75382 Go to UniProtKB: O75382
PHAROS: O75382 GTEx: ENSG00000110171
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O75382
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PE8 Query on PE8 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL C₁₆ H₃₄ O₉ GLZWNFNQMJAZGY-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.80 Å
R-Value Free: 0.321 (Depositor), 0.330 (DCC)
R-Value Work: 0.273 (Depositor), 0.273 (DCC)
R-Value Observed: 0.275 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.9	α = 90
b = 167.9	β = 90
c = 127.2	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
XDS	data reduction
MxCuBE	data collection
PHENIX	phasing
Coot	model building

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-11-15

Deposition Author(s):

Perez-Borrajero, C.

Funding Organization	Location	Grant Number
EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND	Germany	664726
German Research Foundation (DFG)	Germany	HE 7291_1

Revision History (Full details and data files)

Version 1.0: 2023-11-15
Type: Initial release
Version 1.1: 2023-12-20
Changes: Derived calculations
Version 1.2: 2026-03-04
Changes: Refinement description, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.