4UY4 | pdb_00004uy4

1.86 A structure of human Spindlin-4 protein in complex with histone H3K4me3 peptide

PDB DOI: https://doi.org/10.2210/pdb4UY4/pdb

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

Deposited: 2014-08-28 Released: 2014-09-24
Deposition Author(s): Talon, R., Gileadi, C., Johansson, C., Burgess-Brown, N., Shrestha, L., von Delft, F., Krojer, T., Fairhead, M., Bountra, C., Arrowsmith, C.H., Edwards, A., Oppermann, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free:
0.235 (Depositor), 0.232 (DCC)
R-Value Work:
0.202 (Depositor), 0.207 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

1.86 A Structure of Human Spindlin-4 Protein in Complex with Histone H3K4Me3 Peptide

Talon, R., Gileadi, C., Johansson, C., Burgess-Brown, N., Shrestha, L., Fairhead, M., von Delft, F., Krojer, T., Bountra, C., Arrowsmith, C.H., Edwards, A., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 51.35 kDa
Atom Count: 3,625
Modeled Residue Count: 423
Deposited Residue Count: 444
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SPINDLIN-4	A, B	216	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q56A73 (Homo sapiens) Explore Q56A73 Go to UniProtKB: Q56A73
PHAROS: Q56A73 GTEx: ENSG00000186767
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q56A73
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HISTONE H3K4ME3	C, D	6	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431 Go to UniProtKB: P68431
PHAROS: P68431 GTEx: ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775
Entity Groups
UniProt Group	P68431
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
M3L Query on M3L	C, D	L-PEPTIDE LINKING	C₉ H₂₁ N₂ O₂		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.235 (Depositor), 0.232 (DCC)
R-Value Work: 0.202 (Depositor), 0.207 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.072	α = 81.25
b = 51.69	β = 89.89
c = 57.141	γ = 88

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-09-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-09-24
Type: Initial release
Version 1.1: 2015-08-19
Changes: Database references, Structure summary
Version 1.2: 2018-01-24
Changes: Database references, Structure summary
Version 1.3: 2019-05-15
Changes: Data collection, Derived calculations, Experimental preparation
Version 1.4: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Other, Refinement description