[English] 日本語
Yorodumi
- PDB-1zkc: Crystal Structure of the cyclophiln_RING domain of human peptidyl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1zkc
TitleCrystal Structure of the cyclophiln_RING domain of human peptidylprolyl isomerase (cyclophilin)-like 2 isoform b
ComponentsPeptidyl-prolyl cis-trans isomerase like 2
KeywordsISOMERASE / CIS-TRANS ISOMERIZATION / peptidylprolyl isomerase / protein-folding / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


Basigin interactions / ubiquitin-ubiquitin ligase activity / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / protein localization to plasma membrane / RING-type E3 ubiquitin transferase / Golgi lumen / mRNA processing / protein polyubiquitination ...Basigin interactions / ubiquitin-ubiquitin ligase activity / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / protein localization to plasma membrane / RING-type E3 ubiquitin transferase / Golgi lumen / mRNA processing / protein polyubiquitination / ubiquitin protein ligase activity / protein folding / nucleoplasm / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Single helix bin / Peptidyl-prolyl cis-trans isomerase like 2, U-box domain / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / U-box domain profile. / Modified RING finger domain / U-box domain / Cyclophilin-like / Cyclophilin / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. ...Single helix bin / Peptidyl-prolyl cis-trans isomerase like 2, U-box domain / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / U-box domain profile. / Modified RING finger domain / U-box domain / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Beta Barrel / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / RING-type E3 ubiquitin-protein ligase PPIL2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsWalker, J.R. / Davis, T. / Newman, E.M. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: PLoS Biol. / Year: 2010
Title: Structural and biochemical characterization of the human cyclophilin family of peptidyl-prolyl isomerases.
Authors: Davis, T.L. / Walker, J.R. / Campagna-Slater, V. / Finerty, P.J. / Paramanathan, R. / Bernstein, G. / MacKenzie, F. / Tempel, W. / Ouyang, H. / Lee, W.H. / Eisenmesser, E.Z. / Dhe-Paganon, S.
History
DepositionMay 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2018Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase like 2
B: Peptidyl-prolyl cis-trans isomerase like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4944
Polymers44,3382
Non-polymers1562
Water10,467581
1
A: Peptidyl-prolyl cis-trans isomerase like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2472
Polymers22,1691
Non-polymers781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidyl-prolyl cis-trans isomerase like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2472
Polymers22,1691
Non-polymers781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.028, 65.028, 201.790
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Peptidyl-prolyl cis-trans isomerase like 2 / PPIase / Rotamase / Cyclophilin-60 / Cyclophilin-like protein Cyp-60 / cyclophilin-ring domain


Mass: 22168.861 Da / Num. of mol.: 2 / Fragment: sequence databank residues 20-197
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIL2 / Plasmid: pET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q13356, peptidylprolyl isomerase
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 581 / 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: 2.48 Å3/Da / Density % sol: 49.98 %
Crystal growTemperature: 298 K / pH: 7.5
Details: 0.8M Potassium Sodium Tartrate tetrahydrate, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 7.50

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 16, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. obs: 57395 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 31.86
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 1.72 / % possible all: 63.2

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IIP

1iip


Resolution: 1.65→25.97 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.247 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19376 2907 5.1 %RANDOM
Rwork0.15583 ---
obs0.15775 54423 94.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.65→25.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2938 0 0 589 3527
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223014
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.9514064
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6865370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.51223.243148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.28815508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9191526
X-RAY DIFFRACTIONr_chiral_restr0.0950.2430
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022328
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.21406
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22073
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2479
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.282
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.243
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.06431899
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.71342976
X-RAY DIFFRACTIONr_scbond_it4.42751250
X-RAY DIFFRACTIONr_scangle_it4.93171088
X-RAY DIFFRACTIONr_rigid_bond_restr3.49533149
X-RAY DIFFRACTIONr_sphericity_free4.2783582
X-RAY DIFFRACTIONr_sphericity_bonded3.48432946
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 136 -
Rwork0.226 2435 -
obs--59.13 %

+
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