[English] 日本語
Yorodumi
- PDB-4ju5: Crystal structure of the dimeric form of the bb' domains of human... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ju5
TitleCrystal structure of the dimeric form of the bb' domains of human protein disulfide isomerase
ComponentsProtein disulfide-isomerase
KeywordsISOMERASE / thioredoxin-like fold / disulfide isomerase / chaperone
Function / homology
Function and homology information


regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / procollagen-proline 4-dioxygenase complex / VLDL assembly / insulin processing / procollagen-proline 4-dioxygenase activity / interleukin-23-mediated signaling pathway / LDL remodeling / thiol oxidase activity / protein disulfide-isomerase / peptidyl-proline hydroxylation to 4-hydroxy-L-proline ...regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / procollagen-proline 4-dioxygenase complex / VLDL assembly / insulin processing / procollagen-proline 4-dioxygenase activity / interleukin-23-mediated signaling pathway / LDL remodeling / thiol oxidase activity / protein disulfide-isomerase / peptidyl-proline hydroxylation to 4-hydroxy-L-proline / endoplasmic reticulum chaperone complex / Chylomicron assembly / protein folding in endoplasmic reticulum / Collagen biosynthesis and modifying enzymes / Interleukin-23 signaling / interleukin-12-mediated signaling pathway / cellular response to interleukin-7 / Interleukin-12 signaling / Insulin processing / protein disulfide isomerase activity / Detoxification of Reactive Oxygen Species / positive regulation of cell adhesion / protein-disulfide reductase activity / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport / positive regulation of substrate adhesion-dependent cell spreading / response to endoplasmic reticulum stress / Post-translational protein phosphorylation / Hedgehog ligand biogenesis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / melanosome / integrin binding / protein folding / lamellipodium / actin binding / cellular response to hypoxia / positive regulation of viral entry into host cell / cytoskeleton / protein heterodimerization activity / endoplasmic reticulum lumen / external side of plasma membrane / focal adhesion / enzyme binding / endoplasmic reticulum / protein-containing complex / RNA binding / extracellular exosome / extracellular region / cytosol
Similarity search - Function
Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / Endoplasmic reticulum targeting sequence. / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin ...Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / Endoplasmic reticulum targeting sequence. / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein disulfide-isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsBastos-Aristizabal, S. / Kozlov, G. / Gehring, K.
CitationJournal: Protein Sci. / Year: 2014
Title: Structural insight into the dimerization of human protein disulfide isomerase.
Authors: Bastos-Aristizabal, S. / Kozlov, G. / Gehring, K.
History
DepositionMar 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Database references
Revision 1.2Mar 19, 2014Group: Database references
Revision 1.3May 7, 2014Group: Database references
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Sep 20, 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_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein disulfide-isomerase
B: Protein disulfide-isomerase


Theoretical massNumber of molelcules
Total (without water)53,6712
Polymers53,6712
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-32 kcal/mol
Surface area19070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.521, 45.718, 55.149
Angle α, β, γ (deg.)81.85, 92.15, 80.02
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 136 - 347 / Label seq-ID: 7 - 218

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Protein disulfide-isomerase / / PDI / Cellular thyroid hormone-binding protein / Prolyl 4-hydroxylase subunit beta / p55


Mass: 26835.256 Da / Num. of mol.: 2 / Fragment: bb' domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: P4HB, ERBA2L, PDI, PDIA1, PO4DB / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P07237, protein disulfide-isomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 1.85 Å3/Da / Density % sol: 33.59 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 25% (w/v) polyethylene glycol 1500, 25 mM sodium malonate, 37.5 mM imidazole, 37.5 mM boric acid, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 1.7433 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 5, 2007
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7433 Å / Relative weight: 1
ReflectionResolution: 2.28→500 Å / Num. all: 17110 / Num. obs: 15880 / % possible obs: 92.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.5 % / Rsym value: 0.068 / Net I/σ(I): 23.5
Reflection shellResolution: 2.28→2.38 Å / Redundancy: 7 % / Mean I/σ(I) obs: 5.4 / Rsym value: 0.403 / % possible all: 92.7

-
Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3bj5, 3ec3

3bj5

3ec3


Resolution: 2.28→44.55 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.903 / SU B: 8.95 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.556 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28982 836 5.1 %RANDOM
Rwork0.24297 ---
obs0.24533 15714 94.6 %-
all-17110 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.02 Å2
Baniso -1Baniso -2Baniso -3
1-2.03 Å21.88 Å20.17 Å2
2---1.97 Å2-1.05 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 2.28→44.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3034 0 0 67 3101
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193090
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.071.9574180
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7585393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.84425.683139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.32815512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.433156
X-RAY DIFFRACTIONr_chiral_restr0.0720.2486
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212322
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 202 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.18 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.28→2.342 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.468 43 -
Rwork0.39 995 -
obs--81.99 %

+
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