5MR8 | pdb_00005mr8

Crystal structure of TRIM33 PHD-Bromodomain isoform B in complex with H3K9ac histone peptide

PDB DOI: https://doi.org/10.2210/pdb5MR8/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-12-21 Released: 2018-01-17
Deposition Author(s): Tallant, C., Savitsky, P., Fedorov, O., Nunez-Alonso, G., Siejka, P., Krojer, T., Williams, E., Srikannathasan, V., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Muller, S., Knapp, S., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free:
0.286 (Depositor), 0.287 (DCC)
R-Value Work:
0.227 (Depositor), 0.228 (DCC)
R-Value Observed:
0.230 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of TRIM33 PHD-Bromodomain isoform B in complex with H3K9ac histone peptide

Tallant, C., Savitsky, P., Fedorov, O., Nunez-Alonso, G., Siejka, P., Krojer, T., Williams, E., Srikannathasan, V., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Muller, S., Knapp, S.

To be published.

Macromolecule Content

Total Structure Weight: 23.51 kDa
Atom Count: 1,626
Modeled Residue Count: 195
Deposited Residue Count: 203
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase TRIM33	A	194	Homo sapiens	Mutation(s): 0 Gene Names: TRIM33, KIAA1113, RFG7, TIF1G EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UPN9 (Homo sapiens) Explore Q9UPN9 Go to UniProtKB: Q9UPN9
PHAROS: Q9UPN9 GTEx: ENSG00000197323
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UPN9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	B [auth C]	9	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for Q5TEC6 (Homo sapiens) Explore Q5TEC6 Go to UniProtKB: Q5TEC6
Entity Groups
UniProt Group	Q5TEC6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY Query on ALY	B [auth C]	L-PEPTIDE LINKING	C₈ H₁₆ N₂ O₃		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free: 0.286 (Depositor), 0.287 (DCC)
R-Value Work: 0.227 (Depositor), 0.228 (DCC)
R-Value Observed: 0.230 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.885	α = 90
b = 57.994	β = 90
c = 71.488	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-01-17

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2018-01-17
Type: Initial release
Version 1.1: 2018-09-19
Changes: Data collection
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-13
Changes: Structure summary