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- PDB-4qkv: Crystal structure of the mouse cavin1 HR1 domain -

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Basic information

Entry
Database: PDB / ID: 4qkv
TitleCrystal structure of the mouse cavin1 HR1 domain
ComponentsPolymerase I and transcript release factor
KeywordsTRANSCRIPTION / coiled-coil / signalling / plasma membrane
Function / homology
Function and homology information


RNA Polymerase I Transcription Termination / RHOC GTPase cycle / RHOB GTPase cycle / RHOA GTPase cycle / rRNA primary transcript binding / positive regulation of cell motility / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase I promoter / rRNA transcription / protein secretion ...RNA Polymerase I Transcription Termination / RHOC GTPase cycle / RHOB GTPase cycle / RHOA GTPase cycle / rRNA primary transcript binding / positive regulation of cell motility / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase I promoter / rRNA transcription / protein secretion / caveola / endoplasmic reticulum / protein-containing complex / mitochondrion / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Cavin family / PTRF/SDPR family
Similarity search - Domain/homology
Caveolae-associated protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement/SAD / Resolution: 3 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polymerase I and transcript release factor
B: Polymerase I and transcript release factor
C: Polymerase I and transcript release factor


Theoretical massNumber of molelcules
Total (without water)36,8383
Polymers36,8383
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9630 Å2
ΔGint-100 kcal/mol
Surface area17300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.030, 98.690, 104.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Polymerase I and transcript release factor / Cav-p60 / Cavin-1


Mass: 12279.212 Da / Num. of mol.: 3 / Fragment: HR1 domain, UNP residues 45-155
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptrf / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: O54724
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 0.1M HEPES (pH 7.6), 30% MPD, 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: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: Undulator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→52.4 Å / Num. obs: 9020 / % possible obs: 99.7 % / Observed criterion σ(I): 5.4 / Redundancy: 8.3 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 14.9
Reflection shellResolution: 3→3 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 5.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: molecular replacement/SAD / Resolution: 3→37.886 Å / SU ML: 0.39 / σ(F): 1.34 / Phase error: 32.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.283 889 9.94 %
Rwork0.2246 --
obs0.2304 8944 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→37.886 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2162 0 0 13 2175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092162
X-RAY DIFFRACTIONf_angle_d1.282897
X-RAY DIFFRACTIONf_dihedral_angle_d18.796845
X-RAY DIFFRACTIONf_chiral_restr0.045365
X-RAY DIFFRACTIONf_plane_restr0.004370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.18790.32691500.26171306X-RAY DIFFRACTION99
3.1879-3.43390.35621360.23511331X-RAY DIFFRACTION100
3.4339-3.77920.33391520.22281326X-RAY DIFFRACTION100
3.7792-4.32540.21771480.191328X-RAY DIFFRACTION100
4.3254-5.44690.23941450.20831344X-RAY DIFFRACTION99
5.4469-37.88920.3051580.25021420X-RAY DIFFRACTION98
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)
10.76450.3548-1.69831.9947-1.61544.7793-0.2320.22650.1798-0.02940.70880.3102-1-2.4022-0.25140.3292-0.0985-0.1190.99080.18790.63730.868545.966348.8347
20.99190.214-0.96221.1434-2.38837.54140.00470.2640.1573-0.2294-0.15970.0280.1696-0.13870.06220.41570.0429-0.08010.69890.06810.50021.526347.92845.8198
30.33640.22670.2062.4299-2.3133.2044-0.31490.30650.0623-0.48740.52680.1731.1791-2.0312-0.16790.27170.0392-0.00081.01180.13470.48810.856146.263145.6901
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 46:146 )A46 - 146
2X-RAY DIFFRACTION2( CHAIN B AND RESID 52:144 )B52 - 144
3X-RAY DIFFRACTION3( CHAIN C AND RESID 53:143 )C53 - 143

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