[English] 日本語
Yorodumi
- PDB-3r4d: Crystal structure of mouse coronavirus receptor-binding domain co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3r4d
TitleCrystal structure of mouse coronavirus receptor-binding domain complexed with its murine receptor
Components
  • CEA-related cell adhesion molecule 1, isoform 1/2S
  • Spike glycoprotein
KeywordsCELL ADHESION/VIRAL PROTEIN / immunoglobulin / beta-sandwich / mCEACAM1a - immunoglobulin fold MHV spike NTD - galectin-like beta-sandwich fold / mCEACAM1a - cell adhesion MHV spike NTD - mCEACAM1a binding / mCEACAM1a - itself and MHV spike NTD MHV spike NTD - mCEACAM1a / N-glycosylations / mCEACAM1a - 37 / 55 / 70 MHV spike NTD - 192 / CELL ADHESION-VIRAL PROTEIN complex
Function / homology
Function and homology information


Fibronectin matrix formation / granulocyte colony-stimulating factor receptor binding / positive regulation of homophilic cell adhesion / Post-translational modification: synthesis of GPI-anchored proteins / regulation of endothelial cell differentiation / insulin receptor internalization / negative regulation of cytotoxic T cell degranulation / granulocyte colony-stimulating factor signaling pathway / regulation of homophilic cell adhesion / regulation of sprouting angiogenesis ...Fibronectin matrix formation / granulocyte colony-stimulating factor receptor binding / positive regulation of homophilic cell adhesion / Post-translational modification: synthesis of GPI-anchored proteins / regulation of endothelial cell differentiation / insulin receptor internalization / negative regulation of cytotoxic T cell degranulation / granulocyte colony-stimulating factor signaling pathway / regulation of homophilic cell adhesion / regulation of sprouting angiogenesis / regulation of epidermal growth factor receptor signaling pathway / negative regulation of hepatocyte proliferation / regulation of blood vessel remodeling / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of lipid biosynthetic process / negative regulation of T cell mediated cytotoxicity / regulation of endothelial cell migration / negative regulation of granulocyte differentiation / insulin catabolic process / Cell surface interactions at the vascular wall / common myeloid progenitor cell proliferation / Toll-like receptor binding / negative regulation of interleukin-1 production / negative regulation of fatty acid biosynthetic process / cell-cell adhesion via plasma-membrane adhesion molecules / positive regulation of vasculogenesis / bile acid transmembrane transporter activity / regulation of immune system process / negative regulation of platelet aggregation / cell-cell junction organization / negative regulation of vascular permeability / negative regulation of bone resorption / wound healing, spreading of cells / bile acid and bile salt transport / ciliary membrane / negative regulation of cytokine production / microvillus membrane / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of T cell receptor signaling pathway / blood vessel development / negative regulation of osteoclast differentiation / lateral plasma membrane / negative regulation of T cell proliferation / transport vesicle / Neutrophil degranulation / protein tyrosine kinase binding / regulation of ERK1 and ERK2 cascade / basal plasma membrane / regulation of cell growth / adherens junction / negative regulation of protein kinase activity / endocytosis involved in viral entry into host cell / cellular response to insulin stimulus / cell-cell junction / cell junction / virus receptor activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / protein dimerization activity / calmodulin binding / cell adhesion / apical plasma membrane / external side of plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / protein kinase binding / host cell plasma membrane / virion membrane / cell surface / signal transduction / protein homodimerization activity / identical protein binding / membrane / plasma membrane
Similarity search - Function
Spike glycoprotein, N-terminal domain / : / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain ...Spike glycoprotein, N-terminal domain / : / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Jelly Rolls / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Carcinoembryonic antigen-related cell adhesion molecule 1 / CEA-related cell adhesion molecule 1, isoform 1/2S / Spike glycoprotein / Spike glycoprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Murine coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsPeng, G.Q. / Sun, D.W. / Rajashankar, K.R. / Qian, Z.H. / Holmes, K.V. / Li, F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Crystal structure of mouse coronavirus receptor-binding domain complexed with its murine receptor.
Authors: Peng, G. / Sun, D. / Rajashankar, K.R. / Qian, Z. / Holmes, K.V. / Li, F.
History
DepositionMar 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 29, 2014Group: Structure summary
Revision 1.3Apr 15, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp / entity_name_com ...chem_comp / entity_name_com / entity_src_gen / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _chem_comp.type / _entity_name_com.entity_id ..._chem_comp.type / _entity_name_com.entity_id / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _struct_conn.pdbx_leaving_atom_flag / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CEA-related cell adhesion molecule 1, isoform 1/2S
B: Spike glycoprotein
C: CEA-related cell adhesion molecule 1, isoform 1/2S
D: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,10412
Polymers111,9284
Non-polymers2,1768
Water1,22568
1
A: CEA-related cell adhesion molecule 1, isoform 1/2S
B: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0526
Polymers55,9642
Non-polymers1,0884
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: CEA-related cell adhesion molecule 1, isoform 1/2S
D: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0526
Polymers55,9642
Non-polymers1,0884
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.380, 76.380, 942.090
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein CEA-related cell adhesion molecule 1, isoform 1/2S


Mass: 23678.691 Da / Num. of mol.: 2 / Fragment: unp residues 35-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ceacam1, CEACAM1a-2S / Plasmid: pFactbac I / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q3LFS8, UniProt: P31809*PLUS
#2: Protein Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


Mass: 32285.479 Da / Num. of mol.: 2 / Fragment: unp residues 15-296
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine coronavirus / Plasmid: pFactbac I / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: S5ZBM1, UniProt: Q9J3E7*PLUS
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.54 Å3/Da / Density % sol: 65.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10% PEG6000 and 0.2M CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C10.97914
SYNCHROTRONAPS 24-ID-E20.97914
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 33862 / % possible obs: 96.1 % / Rsym value: 0.097 / Net I/σ(I): 20.9
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsRsym valueDiffraction-ID% possible all
3-3.057.66.280.32196.5
3.05-3.11197.7
3.11-3.17199.1
3.17-3.23199.6
3.23-3.3199.5
3.3-3.38199.1
3.38-3.46199.1
3.46-3.56199
3.56-3.66198.9
3.66-3.78199.1
3.78-3.91198.6
3.91-4.07198.8
4.07-4.26197.3
4.26-4.48196
4.48-4.76195.1
4.76-5.13194.2
5.13-5.64195.8
5.64-6.46194.9
6.46-8.13194.6
8.13-50175.2

-
Processing

Software
NameVersionClassification
HKL-3000data collection
SOLVEphasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.1→30 Å / Cor.coef. Fo:Fc: 0.859 / Cor.coef. Fo:Fc free: 0.764 / SU B: 46.905 / SU ML: 0.399 / Cross valid method: THROUGHOUT / ESU R Free: 0.478 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30819 1538 5 %RANDOM
Rwork0.24787 ---
obs-29024 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.772 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.24 Å20 Å2
2--0.48 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 3.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6774 0 140 68 6982
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227104
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.9669706
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0575850
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.81924.241316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.646151080
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6461530
X-RAY DIFFRACTIONr_chiral_restr0.1110.21116
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215412
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_it01.54272
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it026974
X-RAY DIFFRACTIONr_scbond_it2.06832832
X-RAY DIFFRACTIONr_scangle_it3.5734.52732
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellHighest resolution: 3.1 Å / Num. reflection Rwork: 2154 / Total num. of bins used: 20
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.77022.6085-1.1535.6218-4.20299.8247-0.1702-0.29470.25430.00490.33870.0194-0.69870.8763-0.16850.91730.04490.05510.42270.08850.5799-24.009-30.30665.1583
23.58660.16670.244612.5208-4.56510.0283-0.11670.76420.6059-1.0080.08361.37470.0876-1.07730.03310.9505-0.2058-0.0460.68050.20340.9273-24.9211-18.5703-36.8798
32.92226.117-0.676612.8542-0.82368.3766-0.19370.053-0.1251-0.42760.09-0.26520.74890.27030.10371.05430.3455-0.010.37630.2210.4466-30.7161-50.192714.3241
43.11370.4268-1.53812.1738-2.02465.77090.06080.0885-0.0892-0.39530.0531-0.14580.2959-0.0085-0.11390.98320.2888-0.04740.24760.09860.4278-33.1821-56.609424.609
52.72250.8681-0.36894.992-1.46245.33250.0941-0.11740.0928-0.0198-0.0164-0.21560.0750.3526-0.07760.9770.379-0.04610.25890.12870.3651-33.1429-57.21230.02
63.36481.0071-0.26476.6223-3.19667.90610.19010.0212-0.34730.7379-0.133-0.21120.5236-0.3072-0.05710.9889-0.4941-0.02660.26570.05480.6136-0.6788-28.6715-73.3345
77.74993.4323-1.06510.294-0.21297.35820.2819-0.87590.08730.9088-0.3355-0.28360.4087-0.12290.05361.3896-0.460.00450.3580.0880.5242-18.4442-43.0386-35.6848
81.7999-0.8857-1.00620.9214-0.00385.16680.01980.44620.19690.5058-0.17960.10720.256-1.60920.15980.8672-0.39070.08560.65950.05880.4789-7.4486-11.2783-86.367
92.33640.2872-0.51462.0542-0.55565.4754-0.18910.36370.2350.0470.21030.1960.0619-0.777-0.02120.4569-0.32240.09290.40680.11780.4697-5.9481-5.113-97.2672
101.92371.2910.15042.5390.05254.8433-0.18610.41090.2171-0.19610.20380.028-0.2089-0.2865-0.01770.5051-0.37510.12240.44780.10040.4795-3.2439-4.0223-101.8464
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 107
2X-RAY DIFFRACTION2A108 - 199
3X-RAY DIFFRACTION3B15 - 39
4X-RAY DIFFRACTION4B65 - 162
5X-RAY DIFFRACTION5B163 - 268
6X-RAY DIFFRACTION6C1 - 107
7X-RAY DIFFRACTION7C108 - 199
8X-RAY DIFFRACTION8D15 - 39
9X-RAY DIFFRACTION9D65 - 162
10X-RAY DIFFRACTION10D163 - 268

+
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