[English] 日本語
Yorodumi
- PDB-3ich: Crystal structure of cyclophilin B at 1.2 A resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ich
TitleCrystal structure of cyclophilin B at 1.2 A resolution
ComponentsPeptidyl-prolyl cis-trans isomerase B
KeywordsISOMERASE / beta sandwich / Cyclosporin / Endoplasmic reticulum / Glycoprotein / Rotamase
Function / homology
Function and homology information


endoplasmic reticulum chaperone complex / positive regulation by host of viral genome replication / Collagen biosynthesis and modifying enzymes / positive regulation by host of viral process / positive regulation of multicellular organism growth / RNA polymerase binding / cyclosporin A binding / smooth endoplasmic reticulum / protein peptidyl-prolyl isomerization / chaperone-mediated protein folding ...endoplasmic reticulum chaperone complex / positive regulation by host of viral genome replication / Collagen biosynthesis and modifying enzymes / positive regulation by host of viral process / positive regulation of multicellular organism growth / RNA polymerase binding / cyclosporin A binding / smooth endoplasmic reticulum / protein peptidyl-prolyl isomerization / chaperone-mediated protein folding / neutrophil chemotaxis / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / bone development / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / melanosome / protein folding / protein stabilization / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / focal adhesion / perinuclear region of cytoplasm / endoplasmic reticulum / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Cyclophilin-like / Cyclophilin / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsKozlov, G. / Gehring, K.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural Basis of Cyclophilin B Binding by the Calnexin/Calreticulin P-domain.
Authors: Kozlov, G. / Bastos-Aristizabal, S. / Maattanen, P. / Rosenauer, A. / Zheng, F. / Killikelly, A. / Trempe, J.F. / Thomas, D.Y. / Gehring, K.
History
DepositionJul 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase B


Theoretical massNumber of molelcules
Total (without water)20,7361
Polymers20,7361
Non-polymers00
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.665, 64.665, 39.463
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

-
Components

#1: Protein Peptidyl-prolyl cis-trans isomerase B / PPIase / Rotamase / Cyclophilin B / S-cyclophilin / SCYLP / CYP-S1


Mass: 20735.787 Da / Num. of mol.: 1 / Fragment: UNP residues 34-216
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIB, CYPB / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P23284, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 25% w/v PEG 1500, 0.1M MMT buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 30, 2009 / Details: mirrors
RadiationMonochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 54635 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 49.8
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.105 / Mean I/σ(I) obs: 8.8 / Num. unique all: 3989 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1CYN

1cyn


Resolution: 1.2→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.89 / SU ML: 0.019 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.16185 2916 5.1 %RANDOM
Rwork0.14312 ---
all0.14407 54608 --
obs0.14407 54608 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.764 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0.07 Å20 Å2
2---0.14 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1399 0 0 376 1775
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221470
X-RAY DIFFRACTIONr_angle_refined_deg1.1181.9571982
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9215190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.76323.8163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.36615272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.182158
X-RAY DIFFRACTIONr_chiral_restr0.0760.2213
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021104
X-RAY DIFFRACTIONr_nbd_refined0.1780.2694
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21023
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0760.2283
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0710.255
X-RAY DIFFRACTIONr_mcbond_it0.6231.5923
X-RAY DIFFRACTIONr_mcangle_it0.97721457
X-RAY DIFFRACTIONr_scbond_it1.5853611
X-RAY DIFFRACTIONr_scangle_it2.1634.5519
X-RAY DIFFRACTIONr_rigid_bond_restr1.23931534
X-RAY DIFFRACTIONr_sphericity_free1.8853376
X-RAY DIFFRACTIONr_sphericity_bonded1.52231434
LS refinement shellResolution: 1.2→1.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.169 196 -
Rwork0.134 3989 -
obs--99.38 %

+
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