4HEX | pdb_00004hex

A novel conformation of calmodulin

PDB DOI: https://doi.org/10.2210/pdb4HEX/pdb

Classification: CALCIUM BINDING PROTEIN
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-10-04 Released: 2013-03-06
Deposition Author(s): Kumar, V., Chichili, V.P.R., Sivaraman, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.237 (Depositor), 0.253 (DCC)
R-Value Work:
0.210 (Depositor)
R-Value Observed:
0.211 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

A novel trans conformation of ligand-free calmodulin

Kumar, V., Chichili, V.P.R., Tang, X., Sivaraman, J.

(2013) PLoS One 8: e54834-e54834

PubMed: 23382982 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0054834
Primary Citation Related Structures:
4HEX

PubMed Abstract:
Calmodulin (CaM) is a highly conserved eukaryotic protein that binds specifically to more than 100 target proteins in response to calcium (Ca(2+)) signal. CaM adopts a considerable degree of structural plasticity to accomplish this physiological role; however, the nature and extent of this plasticity remain to be fully understood. Here, we report the crystal structure of a novel trans conformation of ligand-free CaM where the relative disposition of two lobes of CaM is different, a conformation to-date not reported. While no major structural changes were observed in the independent N- and C-lobes as compared with previously reported structures of Ca(2+)/CaM, the central helix was tilted by ~90° at Arg75. This is the first crystal structure of CaM to show a drastic conformational change in the central helix, and reveals one of several possible conformations of CaM to engage with its binding partner.

Organizational Affiliation

Department of Biological Sciences, National University of Singapore, Republic of Singapore, Republic of Singapore.

Macromolecule Content

Total Structure Weight: 36.18 kDa
Atom Count: 2,289
Modeled Residue Count: 279
Deposited Residue Count: 312
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calmodulin	A, B	156	Mus musculus	Mutation(s): 0 Gene Names: Cam
UniProt
Find proteins for P0DP26 (Mus musculus) Explore P0DP26 Go to UniProtKB: P0DP26
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DP26
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain H [auth B] SDF format, chain G [auth A] SDF format, chain E [auth A] SDF format, chain C [auth A] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain C [auth A] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain C [auth A]	C [auth A] E [auth A] G [auth A] H [auth B] K [auth B] C [auth A], E [auth A], G [auth A], H [auth B], K [auth B], L [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain K [auth B] Focus chain L [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain F [auth A] SDF format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A]	D [auth A], F [auth A], I [auth B], J [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.237 (Depositor), 0.253 (DCC)
R-Value Work: 0.210 (Depositor)
R-Value Observed: 0.211 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.827	α = 90
b = 116.397	β = 94.83
c = 38.797	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SHELXCD	phasing
SHELXE	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-03-06

Deposition Author(s):

Kumar, V.

Chichili, V.P.R.

Sivaraman, J.

Revision History (Full details and data files)

Version 1.0: 2013-03-06
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2024-03-20
Changes: Data collection, Database references, Derived calculations, Refinement description