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- PDB-4qkw: Crystal structure of the zebrafish cavin4a HR1 domain -

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Basic information

Entry
Database: PDB / ID: 4qkw
TitleCrystal structure of the zebrafish cavin4a HR1 domain
ComponentsMuscle-related coiled-coil protein
KeywordsSIGNALING PROTEIN / coiled-coil / signalling / plasma membrane
Function / homology
Function and homology information


regulation of Rho protein signal transduction / muscle organ development / sarcomere / caveola / regulation of gene expression / cell differentiation / plasma membrane / cytoplasm
Similarity search - Function
Caveolae-associated protein 4 / Cavin family / PTRF/SDPR family
Similarity search - Domain/homology
Caveolae-associated protein 4a
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKovtun, O. / Tillu, V. / Parton, R.G. / Collins, B.M.
CitationJournal: Dev.Cell / Year: 2014
Title: Structural insights into the organization of the cavin membrane coat complex
Authors: Kovtun, O. / Tillu, V.A. / Jung, W. / Leneva, N. / Ariotti, N. / Chaudhary, N. / Mandyam, R.A. / Ferguson, C. / Morgan, G.P. / Johnston, W.A. / Harrop, S.J. / Alexandrov, K. / Parton, R.G. / Collins, B.M.
History
DepositionJun 10, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Muscle-related coiled-coil protein
B: Muscle-related coiled-coil protein
C: Muscle-related coiled-coil protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5844
Polymers36,5493
Non-polymers351
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11020 Å2
ΔGint-100 kcal/mol
Surface area17840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.861, 31.961, 84.764
Angle α, β, γ (deg.)90.00, 94.46, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Muscle-related coiled-coil protein / Muscle-restricted coiled-coil protein


Mass: 12182.922 Da / Num. of mol.: 3 / Fragment: HR1 domain, UNP residues 16-123
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: murc, zgc:158664 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: A1L260
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Hepes (pH 7.5), 20% PEG400, 30% 1,2 propanediol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: 2013
RadiationMonochromator: undulator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.7→45.8 Å / Num. obs: 211025 / % possible obs: 100 % / Observed criterion σ(I): 2.2 / Redundancy: 6.1 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 13
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.826 / Mean I/σ(I) obs: 2.2 / Num. unique all: 30445 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→42.254 Å / SU ML: 0.18 / σ(F): 1.35 / Phase error: 26.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2449 1731 5.04 %
Rwork0.2123 --
obs0.2139 34336 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→42.254 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2333 0 1 238 2572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062359
X-RAY DIFFRACTIONf_angle_d0.833174
X-RAY DIFFRACTIONf_dihedral_angle_d15.768943
X-RAY DIFFRACTIONf_chiral_restr0.05400
X-RAY DIFFRACTIONf_plane_restr0.003406
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.7-1.750.31171410.27222659
1.75-1.80650.30091490.26812691
1.8065-1.87110.27091280.23742708
1.8711-1.9460.26941340.23632659
1.946-2.03460.27471510.23282714
2.0346-2.14180.2571690.21062694
2.1418-2.2760.21821520.19122702
2.276-2.45170.23831370.19092706
2.4517-2.69840.2411350.1912730
2.6984-3.08880.23131420.19992728
3.0888-3.89110.22091420.19542764
3.8911-42.26680.25731510.23332850
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.30260.8896-4.1998-0.4774-0.06632.09850.4850.33150.98860.0377-0.09940.0911-0.1459-0.1368-0.40950.23060.04630.05810.27440.03010.4114-7.197114.039974.9769
26.3797-1.6235-3.6007-0.26210.96121.2555-0.22781.337-0.6889-0.101-0.12220.0593-0.1316-0.5475-0.01170.30260.1495-0.00750.4105-0.01880.312154.05875.420751.8094
32.0870.604-0.46685.91920.21037.0559-0.2251-0.1371-0.9338-0.04090.2882-0.91860.01081.09940.09820.28950.06450.06370.39240.02160.426689.93321.737748.7216
44.0720.0417-1.32160.04020.01850.33920.09240.24580.1345-0.043-0.01780.0078-0.0087-0.0282-0.09270.16590.0439-0.00150.22360.01760.218621.17689.710567.3103
53.8995-3.6451-2.01634.38912.8733.2430.011.0310.2432-0.7174-0.1056-0.6852-0.4077-0.2379-0.03950.3675-0.01620.07370.25660.0170.240386.25517.355738.2409
66.0524-2.267-1.7790.69990.52590.32040.06120.55-0.5957-0.062-0.10530.20480.0268-0.1145-0.02730.22010.0746-0.05460.3179-0.01150.3731-2.38998.265268.4068
75.00891.5384-3.25460.553-1.19962.37970.4948-1.0364-0.74580.1282-0.35950.0181-0.08650.17940.07520.29430.16750.05460.44810.11720.385254.26225.46562.178
82.2742.8957-3.04145.2362-2.57417.72890.1356-0.6231-0.13020.2702-0.2212-0.4358-0.29410.68610.1380.25260.0647-0.04880.2022-0.02310.184782.088310.840752.3289
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 68 )
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 106 )
3X-RAY DIFFRACTION3chain 'A' and (resid 107 through 118 )
4X-RAY DIFFRACTION4chain 'B' and (resid 20 through 105 )
5X-RAY DIFFRACTION5chain 'B' and (resid 106 through 118 )
6X-RAY DIFFRACTION6chain 'C' and (resid 20 through 76 )
7X-RAY DIFFRACTION7chain 'C' and (resid 77 through 96 )
8X-RAY DIFFRACTION8chain 'C' and (resid 97 through 116 )

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