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- PDB-9eg6: Crystal structure of the human Cavin1 HR1 HT/II mutant domain bou... -

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Basic information

Entry
Database: PDB / ID: 9eg6
TitleCrystal structure of the human Cavin1 HR1 HT/II 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 / cytoplasm / cytosol
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: 3.2 Å
AuthorsCollins, B.M. / Gao, Y.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: J.Cell.Sci. / Year: 2025
Title: Nanobodies against Cavin1 reveal structural flexibility and regulated interactions of its N-terminal coiled-coil domain.
Authors: Gao, Y. / Tillu, V.A. / Wu, Y. / Rae, J. / Hall, T.E. / Chen, K.E. / Weeratunga, S. / Guo, Q. / Livingstone, E. / Tham, W.H. / Parton, R.G. / Collins, B.M.
History
DepositionNov 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caveolae-associated protein 1
B: Nanobody B7
C: Caveolae-associated protein 1
D: Nanobody B7
E: Caveolae-associated protein 1
F: Nanobody B7


Theoretical massNumber of molelcules
Total (without water)78,6836
Polymers78,6836
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.315, 59.243, 133.815
Angle α, β, γ (deg.)90.000, 97.477, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 60 through 98)
d_2ens_1chain "C"
d_3ens_1(chain "E" and resid 60 through 98)
d_1ens_2chain "B"
d_2ens_2chain "D"
d_3ens_2chain "F"

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1LEULEULEULEUAA60 - 9822 - 60
d_2ens_1LEULEULEULEUCC60 - 9822 - 60
d_3ens_1LEULEULEULEUEE60 - 9822 - 60
d_1ens_2GLNGLNSERSERBB2 - 1161 - 115
d_2ens_2GLNGLNSERSERDD2 - 1161 - 115
d_3ens_2GLNGLNSERSERFF2 - 1161 - 115

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.498088390574, -0.867107273731, 0.00573855529539), (0.867124216936, -0.498090683042, 0.00112421984211), (0.00188350172439, 0.00553600111867, 0.99998290241)11.8911934308, -7.06309301276, -0.0750366036677
2given(-0.496294968228, 0.868112803584, 0.00845368350557), (-0.868149799549, -0.496299217507, -0.00173558165949), (0.00268887584861, -0.00820042408537, 0.999962760802)11.9599084177, 7.0137951702, 0.0850389211316
3given(-0.498245358246, -0.86702427848, 0.00452366135378), (0.867035639652, -0.498243578862, 0.00159238710139), (0.000873246944821, 0.00471557509724, 0.99998850033)11.9428682763, -7.07119245807, -0.0505398059343
4given(-0.503104363694, 0.864132573265, 0.0126844414028), (-0.864224368009, -0.503074839922, -0.00565218342484), (0.00149698752072, -0.0138058415003, 0.999903574235)11.9214570417, 7.02784181677, 0.0628089600405

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Components

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


Mass: 12706.729 Da / Num. of mol.: 3
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.: 3
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: 2.56 Å3/Da / Density % sol: 51.86 %
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: Feb 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→48 Å / Num. obs: 13349 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 59.38 Å2 / CC1/2: 0.991 / Rpim(I) all: 0.116 / Net I/σ(I): 6.6
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2402 / CC1/2: 0.878 / Rpim(I) all: 0.502 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→44.23 Å / SU ML: 0.414 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.5282
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2867 721 5.43 %
Rwork0.2581 12559 -
obs0.2597 13280 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 105.15 Å2
Refinement stepCycle: LAST / Resolution: 3.2→44.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3597 0 0 0 3597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00673642
X-RAY DIFFRACTIONf_angle_d0.86964922
X-RAY DIFFRACTIONf_chiral_restr0.0511556
X-RAY DIFFRACTIONf_plane_restr0.011646
X-RAY DIFFRACTIONf_dihedral_angle_d14.6091343
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.129745118387
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.365970733942
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.116027331418
ens_2d_3BBX-RAY DIFFRACTIONTorsion NCS0.111149760434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.450.42651540.35932479X-RAY DIFFRACTION99.36
3.45-3.790.32741330.31972479X-RAY DIFFRACTION98.94
3.79-4.340.25491500.24462478X-RAY DIFFRACTION99.06
4.34-5.470.21741420.19992529X-RAY DIFFRACTION99.55
5.47-44.230.27951420.23812594X-RAY DIFFRACTION99.64

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