6JBK | pdb_00006jbk

Crystal structure of an actin monomer in complex with the nucleator Cordon-Bleu WH2-motif peptide mutant. T22V

PDB DOI: https://doi.org/10.2210/pdb6JBK/pdb

Classification: STRUCTURAL PROTEIN/PROTEIN BINDING
Organism(s): Oryctolagus cuniculus, Mus musculus
Expression System: Escherichia coli, Escherichia coli BL21
Mutation(s): Yes

Deposited: 2019-01-25 Released: 2020-02-05
Deposition Author(s): Scipion, C.P.M., Robinson, R.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.239 (Depositor), 0.242 (DCC)
R-Value Work:
0.187 (Depositor), 0.194 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Design of an actin-severing peptide

Scipion, C.P.M., Robinson, R.C.

To be published.

Macromolecule Content

Total Structure Weight: 180.44 kDa
Atom Count: 12,277
Modeled Residue Count: 1,500
Deposited Residue Count: 1,596
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, alpha skeletal muscle	A, C, E, G	377	Oryctolagus cuniculus	Mutation(s): 0 Gene Names: ACTA1, ACTA EC: 3.6.4
UniProt
Find proteins for P68135 (Oryctolagus cuniculus) Explore P68135 Go to UniProtKB: P68135
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68135
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide from Protein cordon-bleu	B, D, F, H	22	Mus musculus	Mutation(s): 1 Gene Names: Cobl, Kiaa0633
UniProt & NIH Common Fund Data Resources
Find proteins for Q5NBX1 (Mus musculus) Explore Q5NBX1 Go to UniProtKB: Q5NBX1
IMPC: MGI:105056
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5NBX1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain R [auth G] SDF format, chain O [auth E] SDF format, chain L [auth C] SDF format, chain I [auth A] MOL2 format, chain R [auth G] MOL2 format, chain O [auth E] MOL2 format, chain L [auth C] MOL2 format, chain I [auth A] mmCIF format, chain R [auth G] mmCIF format, chain O [auth E] mmCIF format, chain L [auth C] mmCIF format, chain I [auth A]	I [auth A], L [auth C], O [auth E], R [auth G]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain I [auth A] Focus chain L [auth C] Focus chain O [auth E] Focus chain R [auth G] Interactions & Density Focus chain I [auth A] Focus chain L [auth C] Focus chain O [auth E] Focus chain R [auth G]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain T [auth G] SDF format, chain S [auth G] SDF format, chain Q [auth E] SDF format, chain P [auth E] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain T [auth G] MOL2 format, chain S [auth G] MOL2 format, chain Q [auth E] MOL2 format, chain P [auth E] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain T [auth G] mmCIF format, chain S [auth G] mmCIF format, chain Q [auth E] mmCIF format, chain P [auth E] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	J [auth A] K [auth A] M [auth C] N [auth C] P [auth E] J [auth A], K [auth A], M [auth C], N [auth C], P [auth E], Q [auth E], S [auth G], T [auth G]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth E] Focus chain Q [auth E] Focus chain S [auth G] Focus chain T [auth G] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth E] Focus chain Q [auth E] Focus chain S [auth G] Focus chain T [auth G]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HIC Query on HIC	A, C, E, G	L-PEPTIDE LINKING	C₇ H₁₁ N₃ O₂		HIS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.239 (Depositor), 0.242 (DCC)
R-Value Work: 0.187 (Depositor), 0.194 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.22	α = 90.62
b = 81.192	β = 107.19
c = 89.869	γ = 109.63

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-02-05

Deposition Author(s):

Scipion, C.P.M.

Robinson, R.C.

Revision History (Full details and data files)

Version 1.0: 2020-02-05
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description

6JBK | pdb_00006jbk

Crystal structure of an actin monomer in complex with the nucleator Cordon-Bleu WH2-motif peptide mutant. T22V

Literature

Design of an actin-severing peptide

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt & NIH Common Fund Data Resources