[English] 日本語
Yorodumi
- PDB-9wqu: b-b' domain fragment of ER-60 (ERp57) under microgravity -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9wqu
Titleb-b' domain fragment of ER-60 (ERp57) under microgravity
ComponentsProtein disulfide-isomerase A3
KeywordsISOMERASE / thioredoxin fold / endoplasmic reticulum / oxidative protein folding
Function / homology
Function and homology information


Tapasin-ERp57 complex / Calnexin/calreticulin cycle / protein disulfide-isomerase / protein folding in endoplasmic reticulum / disulfide oxidoreductase activity / C-type glycerophospholipase activity / cellular response to interleukin-7 / positive regulation of extrinsic apoptotic signaling pathway / protein disulfide isomerase activity / lncRNA binding ...Tapasin-ERp57 complex / Calnexin/calreticulin cycle / protein disulfide-isomerase / protein folding in endoplasmic reticulum / disulfide oxidoreductase activity / C-type glycerophospholipase activity / cellular response to interleukin-7 / positive regulation of extrinsic apoptotic signaling pathway / protein disulfide isomerase activity / lncRNA binding / protein-disulfide reductase activity / phagocytic vesicle / extrinsic apoptotic signaling pathway / response to endoplasmic reticulum stress / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class I protein complex / MHC class I peptide loading complex / platelet aggregation / recycling endosome membrane / melanosome / protein folding / ER-Phagosome pathway / adaptive immune response / endoplasmic reticulum lumen / cysteine-type endopeptidase activity / focal adhesion / cell surface / endoplasmic reticulum / extracellular space / RNA binding / extracellular exosome / identical protein binding / nucleus
Similarity search - Function
Protein disulfide-isomerase A3, first redox inactive TRX-like domain b / Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
Protein disulfide-isomerase A3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFurubayashi, N. / Shinohara, Y. / Inaka, K. / Kaito, S. / Kobayashi, Y. / Kamo, M. / Urade, R.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18380079 Japan
Japan Society for the Promotion of Science (JSPS)21380081 Japan
Japan Society for the Promotion of Science (JSPS)25292070 Japan
CitationJournal: To Be Published
Title: Crystal structure of b-b' domain fragment of ER-60 (ERp57) under microgravity
Authors: Furubayashi, N. / Shinohara, Y. / Inaka, K. / Kaito, S. / Kobayashi, Y. / Kamo, M. / Urade, R.
History
DepositionSep 11, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein disulfide-isomerase A3
B: Protein disulfide-isomerase A3
C: Protein disulfide-isomerase A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,9445
Polymers85,7523
Non-polymers1922
Water9,620534
1
A: Protein disulfide-isomerase A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6802
Polymers28,5841
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein disulfide-isomerase A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6802
Polymers28,5841
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein disulfide-isomerase A3


Theoretical massNumber of molelcules
Total (without water)28,5841
Polymers28,5841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.315, 62.901, 97.148
Angle α, β, γ (deg.)90.00, 98.64, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Protein disulfide-isomerase A3 / 58 kDa glucose-regulated protein / 58 kDa microsomal protein / p58 / Disulfide isomerase ER-60 / ...58 kDa glucose-regulated protein / 58 kDa microsomal protein / p58 / Disulfide isomerase ER-60 / Endoplasmic reticulum resident protein 57 / ER protein 57 / ERp57 / Endoplasmic reticulum resident protein 60 / ER protein 60 / ERp60


Mass: 28584.018 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDIA3, ERP57, ERP60, GRP58 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P30101, protein disulfide-isomerase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 534 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.01 %
Crystal growTemperature: 293 K / Method: counter-diffusion / pH: 7
Details: 50 mM HEPES-NaOH, pH 7.0, 20% PEG3350, 50 mM Ammonium Sulfate, 100 m M NaCl, 0.04% NaN3

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.75 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.75 Å / Relative weight: 1
ReflectionResolution: 1.8→90 Å / Num. obs: 82113 / % possible obs: 99.4 % / Redundancy: 3.84 % / CC1/2: 0.999 / Rmerge(I) obs: 0.029 / Rrim(I) all: 0.041 / Net I/σ(I): 9.31
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.8-1.910.29792930.8240.421
1.91-2.040.14990950.9420.2111
2.04-2.20.08685280.9810.1221
2.2-2.410.05379520.9920.0751
2.41-2.70.03672280.9960.0521
2.7-3.110.02363770.9980.0321
3.11-3.810.01753690.9990.0231
3.81-5.370.01342590.9990.0191
5.37-47.780.01422170.9990.0191

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H8L

2h8l


Resolution: 1.8→47.78 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.765 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26272 4065 5 %RANDOM
Rwork0.21863 ---
obs0.22081 78026 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.707 Å2
Baniso -1Baniso -2Baniso -3
1-7.18 Å20 Å2-1.39 Å2
2---7.97 Å2-0 Å2
3---0.79 Å2
Refinement stepCycle: 1 / Resolution: 1.8→47.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5673 0 10 534 6217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0125805
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0351.8417793
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8285698
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.141533
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14101057
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1410.2816
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024415
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6063.2712795
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.5295.8613489
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.6183.6433010
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.49242.128984
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å
RfactorNum. reflection% reflection
Rfree0.376 298 -
Rwork0.273 5567 -
obs--97.01 %

+
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