[English] 日本語
Yorodumi
- PDB-9egn: Crystal structure of the human Cavin1 HR1 domain bound to nanobody B7 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9egn
TitleCrystal structure of the human Cavin1 HR1 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: 1.57 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 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)26,2412
Polymers26,2412
Non-polymers00
Water2,522140
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)78,7226
Polymers78,7226
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)58.897, 58.897, 113.122
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11B-319-

HOH

21B-319-

HOH

31B-320-

HOH

-
Components

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


Mass: 12719.664 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)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.65 M potassium thiocyanate, 19.5% PEG 2000 MME

-
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: 1.57→46 Å / Num. obs: 31084 / % possible obs: 99.7 % / Redundancy: 20 % / Biso Wilson estimate: 21.85 Å2 / CC1/2: 1 / Rpim(I) all: 0.1 / Net I/σ(I): 28.3
Reflection shellResolution: 1.57→1.6 Å / Mean I/σ(I) obs: 4 / Num. unique obs: 1492 / CC1/2: 0.96 / Rpim(I) all: 0.107

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→37.88 Å / SU ML: 0.148 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 19.9596
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1904 2001 6.45 %
Rwork0.1727 29043 -
obs0.1738 31044 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.87 Å2
Refinement stepCycle: LAST / Resolution: 1.57→37.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1211 0 0 140 1351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01151226
X-RAY DIFFRACTIONf_angle_d1.37161657
X-RAY DIFFRACTIONf_chiral_restr0.0899188
X-RAY DIFFRACTIONf_plane_restr0.0142217
X-RAY DIFFRACTIONf_dihedral_angle_d14.6091452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.610.23991400.21582009X-RAY DIFFRACTION97.11
1.61-1.650.21711430.19342080X-RAY DIFFRACTION100
1.65-1.70.21471450.19112062X-RAY DIFFRACTION100
1.7-1.750.22261400.1832082X-RAY DIFFRACTION100
1.75-1.820.23621380.18182066X-RAY DIFFRACTION99.95
1.82-1.890.18521420.19542075X-RAY DIFFRACTION100
1.89-1.980.20431480.18222080X-RAY DIFFRACTION100
1.98-2.080.18931410.18012066X-RAY DIFFRACTION100
2.08-2.210.20511400.1812090X-RAY DIFFRACTION100
2.21-2.380.22091420.17062081X-RAY DIFFRACTION100
2.38-2.620.20321480.18312067X-RAY DIFFRACTION99.95
2.62-30.20161430.17532081X-RAY DIFFRACTION100
3-3.780.17871410.17152100X-RAY DIFFRACTION100
3.78-37.880.16011500.15272104X-RAY DIFFRACTION99.78

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more