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- PDB-9eiu: Crystal structure of the human Cavin1 HR1 TS/DD mutant domain bou... -

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Basic information

Entry
Database: PDB / ID: 9eiu
TitleCrystal structure of the human Cavin1 HR1 TS/DD mutant domain bound to nanobody B7
Components
  • Caveolae-associated protein 1
  • Nanobody B7
KeywordsPROTEIN TRANSPORT / Caveolae / Cavin1 / nanobody
Function / homology
Function and homology information


rRNA primary transcript binding / RNA Polymerase I Transcription Termination / positive regulation of cell motility / RHOB GTPase cycle / RHOC GTPase cycle / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase I promoter / rRNA transcription / protein secretion / RHOA GTPase cycle ...rRNA primary transcript binding / RNA Polymerase I Transcription Termination / positive regulation of cell motility / RHOB GTPase cycle / RHOC GTPase cycle / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase I promoter / rRNA transcription / protein secretion / RHOA GTPase cycle / caveola / membrane raft / intracellular membrane-bounded organelle / endoplasmic reticulum / protein-containing complex / mitochondrion / RNA binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Cavin family / PTRF/SDPR family
Similarity search - Domain/homology
Caveolae-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsCollins, B.M. / Gao, Y.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: To Be Published
Title: Crystal structure of the human Cavin1 HR1 domain bound to nanobody B7
Authors: Collins, B.M. / Gao, Y.
History
DepositionNov 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Caveolae-associated protein 1
B: Nanobody B7


Theoretical massNumber of molelcules
Total (without water)26,2832
Polymers26,2832
Non-polymers00
Water00
1
A: Caveolae-associated protein 1
B: Nanobody B7

A: Caveolae-associated protein 1
B: Nanobody B7

A: Caveolae-associated protein 1
B: Nanobody B7


Theoretical massNumber of molelcules
Total (without water)78,8486
Polymers78,8486
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area10190 Å2
ΔGint-62 kcal/mol
Surface area20450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.669, 58.669, 61.293
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3
Space group name HallP3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z

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Components

#1: Protein Caveolae-associated protein 1 / Cavin-1 / Polymerase I and transcript release factor


Mass: 12761.657 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAVIN1, PTRF, FKSG13 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NZI2
#2: Antibody Nanobody B7


Mass: 13520.991 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
Has protein modificationN

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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: 2.32 Å3/Da / Density % sol: 46.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M potassium thiocyanate, 20% PEG 3350 and 0.2 M potassium citrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4→30.65 Å / Num. obs: 1975 / % possible obs: 99.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 94.34 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.037 / Net I/σ(I): 7.9
Reflection shellResolution: 4→4.5 Å / Num. unique obs: 572 / CC1/2: 0.99 / Rpim(I) all: 0.077

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4→30.65 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 2.06 / Phase error: 31.1874
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2635 130 6.58 %
Rwork0.2025 1845 -
obs0.2063 1975 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 183.05 Å2
Refinement stepCycle: LAST / Resolution: 4→30.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1211 0 0 0 1211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411226
X-RAY DIFFRACTIONf_angle_d0.78621657
X-RAY DIFFRACTIONf_chiral_restr0.0485188
X-RAY DIFFRACTIONf_plane_restr0.0097217
X-RAY DIFFRACTIONf_dihedral_angle_d14.5354452
LS refinement shellResolution: 4→30.65 Å
RfactorNum. reflection% reflection
Rfree0.2635 130 -
Rwork0.2025 1845 -
obs--98.95 %

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