[English] 日本語
Yorodumi
- PDB-1ogt: CRYSTAL STRUCTURE OF HLA-B*2705 COMPLEXED WITH THE VASOACTIVE INT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ogt
TitleCRYSTAL STRUCTURE OF HLA-B*2705 COMPLEXED WITH THE VASOACTIVE INTESTINAL PEPTIDE TYPE 1 RECEPTOR (VIPR) PEPTIDE (RESIDUES 400-408)
Components
  • BETA-2-MICROGLOBULIN
  • HLA CLASS I HISTOCOMPATIBILITY ANTIGEN
  • VASOACTIVE INTESTINAL POLYPEPTIDE RECEPTOR 1
KeywordsIMMUNE SYSTEM / IMMUNE SYSTEM-COMPLEX / MHC (MAJOR HISTOCOMPATIBILITY COMPLEX) / HLA- B*2705
Function / homology
Function and homology information


: / : / : / : / : / negative regulation of receptor binding / pituitary adenylate cyclase-activating polypeptide receptor activity / vasoactive intestinal polypeptide receptor activity / regulation of interleukin-12 production / regulation of dendritic cell differentiation ...: / : / : / : / : / negative regulation of receptor binding / pituitary adenylate cyclase-activating polypeptide receptor activity / vasoactive intestinal polypeptide receptor activity / regulation of interleukin-12 production / regulation of dendritic cell differentiation / retina homeostasis / regulation of T cell anergy / G protein-coupled peptide receptor activity / regulation of interleukin-6 production / positive regulation of protein binding / regulation of membrane depolarization / protection from natural killer cell mediated cytotoxicity / peptide hormone binding / TAP binding / detection of bacterium / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / secretory granule membrane / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / response to molecule of bacterial origin / HFE-transferrin receptor complex / transferrin transport / defense response / MHC class I peptide loading complex / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / cellular response to nicotine / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / specific granule lumen / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / phagocytic vesicle membrane / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / recycling endosome membrane / positive regulation of T cell activation / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / positive regulation of cellular senescence / sensory perception of smell / tertiary granule lumen / Glucagon-type ligand receptors / MHC class II protein complex binding / DAP12 signaling / T cell differentiation in thymus / antimicrobial humoral immune response mediated by antimicrobial peptide / late endosome membrane / negative regulation of neuron projection development / antibacterial humoral response / adenylate cyclase-activating G protein-coupled receptor signaling pathway / protein refolding / protein-folding chaperone binding / ER-Phagosome pathway / cellular response to lipopolysaccharide / early endosome membrane / G alpha (s) signalling events / amyloid fibril formation / protein homotetramerization / defense response to Gram-negative bacterium / intracellular iron ion homeostasis / adaptive immune response / learning or memory / cell surface receptor signaling pathway / signaling receptor complex / defense response to Gram-positive bacterium / immune response / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen
Similarity search - Function
GPCR, family 2, vasoactive intestinal peptide receptor 1 / GPCR, family 2, vasoactive intestinal peptide receptor / G-protein coupled receptors family 2 signature 1. / : / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / Hormone receptor domain / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. ...GPCR, family 2, vasoactive intestinal peptide receptor 1 / GPCR, family 2, vasoactive intestinal peptide receptor / G-protein coupled receptors family 2 signature 1. / : / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / Hormone receptor domain / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Beta-2-microglobulin / HLA class I histocompatibility antigen, B alpha chain / HLA class I histocompatibility antigen, B alpha chain / Vasoactive intestinal polypeptide receptor 1 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsHulsmeyer, M. / Fiorillo, M.T. / Bettosini, F. / Sorrentino, R. / Saenger, W. / Ziegler, A. / Uchanska-Ziegler, B.
Citation
Journal: J. Exp. Med. / Year: 2004
Title: Dual, HLA-B27 subtype-dependent conformation of a self-peptide.
Authors: Hulsmeyer, M. / Fiorillo, M.T. / Bettosini, F. / Sorrentino, R. / Saenger, W. / Ziegler, A. / Uchanska-Ziegler, B.
#1: Journal: J.Biol.Chem. / Year: 2002
Title: Hla-B27 Subtypes Differentially Associated with Disease Exhibit Subtle Structural Alterations
Authors: Hulsmeyer, M. / Hillig, R.C. / Volz, A. / Ruhl, M. / Schroder, W. / Saenger, W. / Ziegler, A. / Uchanska-Ziegler, B.
#2: Journal: Cell(Cambridge,Mass.) / Year: 1992
Title: The Three-Dimensional Structure of Hla-B27 at 2.1 A Resolution Suggests a General Mechanism for Tight Peptide Binding to Mhc
Authors: Madden, D.R. / Gorga, J.C. / Strominger, J.L. / Wiley, D.C.
History
DepositionMay 13, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 19, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / struct_conn / struct_conn_type
Item: _atom_site.label_alt_id / _atom_site_anisotrop.pdbx_label_alt_id ..._atom_site.label_alt_id / _atom_site_anisotrop.pdbx_label_alt_id / _citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title
Revision 2.1May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 2.2May 22, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 2.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN
B: BETA-2-MICROGLOBULIN
C: VASOACTIVE INTESTINAL POLYPEPTIDE RECEPTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7239
Polymers45,2073
Non-polymers5156
Water12,989721
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.259, 81.777, 65.617
Angle α, β, γ (deg.)90.00, 107.61, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein HLA CLASS I HISTOCOMPATIBILITY ANTIGEN / B-27 B*2705 ALPHA CHAIN / HUMAN LEUCOCYTE ANTIGEN B*2705 HEAVY CHAIN


Mass: 31928.160 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P10318, UniProt: P01889*PLUS
#2: Protein BETA-2-MICROGLOBULIN / HDCMA22P


Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P01884, UniProt: P61769*PLUS

-
Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide VASOACTIVE INTESTINAL POLYPEPTIDE RECEPTOR 1 / VPAC1 / VIP-R-1 / PITUITARY ADENYLATE CYCLASE ACTIVATING POLYPEPTIDE TYPE II RECEPTOR / PACAP TYPE ...VPAC1 / VIP-R-1 / PITUITARY ADENYLATE CYCLASE ACTIVATING POLYPEPTIDE TYPE II RECEPTOR / PACAP TYPE II RECEPTOR / PACAP-R-2


Mass: 1399.694 Da / Num. of mol.: 1 / Fragment: RESIDUES 400-408 / Source method: obtained synthetically / Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESISED / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P32241

-
Non-polymers , 3 types, 727 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 721 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsB*2705:INVOLVED IN THE PRESENTATION OF FOREIGN ANTIGENS TO THE IMMUNE SYSTEM. B*2075 MOLECULES ...B*2705:INVOLVED IN THE PRESENTATION OF FOREIGN ANTIGENS TO THE IMMUNE SYSTEM. B*2075 MOLECULES EXIST AS HETEROTRIMERS CONSISTING OF HEAVY CHAIN (CHAINID A), LIGHT CHAIN (BETA-2- MICROGLOBULIN) AND PEPTIDE
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 56.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: TRIS PH 8.0, 16% PEG 8000, HANGING DROP, TEMPERATURE 291K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails (eV)Chemical formula
10.1 MTris-HCl1reservoirpH8.0
216 %PEG80001reservoir
320 mg/mlprotein1drop
410 mMTris-HCl1droppH7.5
5150 mM1dropNaCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.898
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 25, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.898 Å / Relative weight: 1
ReflectionResolution: 1.47→50 Å / Num. obs: 84476 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 13.3
Reflection shellResolution: 1.47→1.53 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 2.2 / % possible all: 95.2
Reflection
*PLUS
Highest resolution: 1.47 Å / Lowest resolution: 50 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
% possible obs: 95.2 % / Redundancy: 3.3 % / Num. unique obs: 8185 / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 2.2

-
Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OF2

1of2


Resolution: 1.47→62.02 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.017 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.178 4249 5 %RANDOM
Rwork0.128 ---
obs0.131 80199 96.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20.23 Å2
2---0.28 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.47→62.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3189 0 31 721 3941
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213506
X-RAY DIFFRACTIONr_bond_other_d0.0020.023039
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.9264760
X-RAY DIFFRACTIONr_angle_other_deg0.87437085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3065395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.090.2483
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023873
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02775
X-RAY DIFFRACTIONr_nbd_refined0.2230.2591
X-RAY DIFFRACTIONr_nbd_other0.2590.23566
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.080.22033
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.2509
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3070.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.244
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.58821995
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.81333251
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.68621511
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it9.66931508
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 1.47→1.51 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.286 264
Rwork0.184 5031
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.4
LS refinement shell
*PLUS
Rfactor Rfree: 0.286 / Rfactor Rwork: 0.184

+
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