4ZLK | pdb_00004zlk

Crystal structure of mouse myosin-5a in complex with calcium-bound calmodulin

PDB DOI: https://doi.org/10.2210/pdb4ZLK/pdb

Classification: MOTOR PROTEIN/METAL BINDING PROTEIN
Organism(s): Mus musculus
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2015-05-01 Released: 2016-05-04
Deposition Author(s): Shen, M., Zhang, N., Zheng, S., Zhang, W.-B., Zhang, H.-M., Lu, Z., Su, Q.P., Sun, Y., Ye, K., Li, X.-D.
Funding Organization(s): National Basic Research Program of China, National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.246 (Depositor), 0.250 (DCC)
R-Value Work:
0.196 (Depositor), 0.200 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Structural basis for calcium regulation of myosin 5 motor function

Shen, M., Zheng, S., Zhang, W., Lu, Z., Ye, K., Li, X.

To be published.

Macromolecule Content

Total Structure Weight: 113.84 kDa
Atom Count: 7,289
Modeled Residue Count: 866
Deposited Residue Count: 988
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Unconventional myosin-Va	A	839	Mus musculus	Mutation(s): 0 Gene Names: Myo5a, Dilute
UniProt & NIH Common Fund Data Resources
Find proteins for Q99104 (Mus musculus) Explore Q99104 Go to UniProtKB: Q99104
IMPC: MGI:105976
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q99104
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Calmodulin	B	149	Mus musculus	Mutation(s): 0 Gene Names: Calm1, Calm, Cam, Cam1, Calm2, Cam2, Camb, Calm3, Cam3, Camc
UniProt
Find proteins for P0DP26 (Mus musculus) Explore P0DP26 Go to UniProtKB: P0DP26
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DP26
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth B] SDF format, chain D [auth B] SDF format, chain C [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] MOL2 format, chain D [auth B] MOL2 format, chain C [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B] mmCIF format, chain D [auth B] mmCIF format, chain C [auth B]	C [auth B], D [auth B], E [auth B], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.246 (Depositor), 0.250 (DCC)
R-Value Work: 0.196 (Depositor), 0.200 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.079	α = 90
b = 99.455	β = 90
c = 248.159	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2016-05-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Basic Research Program of China	China	2013CB932802
National Basic Research Program of China	China	2012CB114102
National Natural Science Foundation of China	China	31171367
National Natural Science Foundation of China	China	31470791
National Natural Science Foundation of China	China	31325007

Revision History (Full details and data files)

Version 1.0: 2016-05-04
Type: Initial release
Version 1.1: 2016-10-05
Changes: Structure summary
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description