[English] 日本語
Yorodumi
- PDB-3d0h: Crystal structure of spike protein receptor-binding domain from t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3d0h
TitleCrystal structure of spike protein receptor-binding domain from the 2002-2003 SARS coronavirus civet strain complexed with human-civet chimeric receptor ACE2
Components
  • Angiotensin-converting enzyme 2
  • Spike glycoproteinSpike protein
KeywordsHYDROLASE / SARS coronavirus / spike protein / receptor-binding domain / RBD / angiotensin-converting enzyme 2 / ACE2 / virus-host interface / host adaptation / cross-species infections / human / palm civet / Carboxypeptidase / Chloride / Glycoprotein / Membrane / Metal-binding / Metalloprotease / Protease / Secreted / Transmembrane / Envelope protein / Host-virus interaction / Lipoprotein / Palmitate / Virion / Virulence
Function / homology
Function and homology information


Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / tryptophan transport / positive regulation of gap junction assembly ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / tryptophan transport / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / regulation of vasoconstriction / regulation of cardiac conduction / peptidyl-dipeptidase activity / angiotensin maturation / maternal process involved in female pregnancy / Metabolism of Angiotensinogen to Angiotensins / metallocarboxypeptidase activity / Attachment and Entry / negative regulation of signaling receptor activity / carboxypeptidase activity / regulation of cytokine production / positive regulation of cardiac muscle contraction / viral life cycle / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / regulation of transmembrane transporter activity / brush border membrane / cilium / endocytosis involved in viral entry into host cell / negative regulation of ERK1 and ERK2 cascade / endocytic vesicle membrane / SARS-CoV-1 activates/modulates innate immune responses / metallopeptidase activity / positive regulation of reactive oxygen species metabolic process / virus receptor activity / regulation of cell population proliferation / regulation of inflammatory response / endopeptidase activity / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / Potential therapeutics for SARS / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont entry into host cell / membrane raft / apical plasma membrane / fusion of virus membrane with host plasma membrane / endoplasmic reticulum lumen / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell plasma membrane / virion membrane / cell surface / proteolysis / extracellular space / extracellular exosome / zinc ion binding / extracellular region / membrane / identical protein binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Spike protein, C-terminal core receptor binding subdomain / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Collectrin-like domain profile. / Collectrin domain / Renal amino acid transporter / Peptidase family M2 domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Neutral zinc metallopeptidases, zinc-binding region signature. / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like ...Spike protein, C-terminal core receptor binding subdomain / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Collectrin-like domain profile. / Collectrin domain / Renal amino acid transporter / Peptidase family M2 domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Neutral zinc metallopeptidases, zinc-binding region signature. / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-glucopyranose / Spike glycoprotein / Angiotensin-converting enzyme 2 / Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesPaguma larvata (masked palm civet)
Homo sapiens (human)
Human SARS coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1 Å
AuthorsLi, F.
CitationJournal: J.Virol. / Year: 2008
Title: Structural analysis of major species barriers between humans and palm civets for severe acute respiratory syndrome coronavirus infections
Authors: Li, F.
History
DepositionMay 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jun 14, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name / _struct_ref_seq_dif.details
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_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Angiotensin-converting enzyme 2
B: Angiotensin-converting enzyme 2
E: Spike glycoprotein
F: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,52414
Polymers178,9954
Non-polymers1,52910
Water48627
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Angiotensin-converting enzyme 2
E: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,0416
Polymers89,4982
Non-polymers5434
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-49 kcal/mol
Surface area33780 Å2
MethodPISA
3
B: Angiotensin-converting enzyme 2
F: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4838
Polymers89,4982
Non-polymers9866
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-39.9 kcal/mol
Surface area34090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.352, 119.841, 109.420
Angle α, β, γ (deg.)90.00, 95.89, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
12A
22B
32A
42B
52A
62B
13E
23F

NCS domain segments:

Refine code: 6

Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERGLNAA19 - 1021 - 84
211SERGLNBB19 - 1021 - 84
321ASNASNAA290 - 397272 - 379
421ASNASNBB290 - 397272 - 379
531HISGLUAA417 - 430399 - 412
631HISGLUBB417 - 430399 - 412
112ASNPROAA103 - 28985 - 271
212ASNPROBB103 - 28985 - 271
322GLULYSAA398 - 416380 - 398
422GLULYSBB398 - 416380 - 398
532ASPASPAA431 - 615413 - 597
632ASPASPBB431 - 615413 - 597
113PROGLUEC324 - 5021 - 179
213PROGLUFD324 - 5021 - 179

NCS ensembles :
ID
1
2
3

-
Components

-
Protein , 2 types, 4 molecules ABEF

#1: Protein Angiotensin-converting enzyme 2 / / ACE-related carboxypeptidase / Angiotensin-converting enzyme homolog / ACEH / Metalloprotease MPROT15


Mass: 69076.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paguma larvata (masked palm civet), (gene. exp.) Homo sapiens (human)
Gene: ACE2, ACE2, UNQ868/PRO1885 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q56NL1, UniProt: Q9BYF1, angiotensin-converting enzyme 2
#2: Protein Spike glycoprotein / Spike protein / S glycoprotein / E2 / Peplomer protein


Mass: 20420.982 Da / Num. of mol.: 2 / Fragment: residues 324-502
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human SARS coronavirus / Gene: S, 2 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P59594

-
Sugars , 2 types, 6 molecules

#3: Sugar
ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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

-
Non-polymers , 3 types, 31 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.93 Å3/Da / Density % sol: 57.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 100 mM Tris, 22% PEG6000, 100 mM NaCl, pH 8.5, vapor diffusion, temperature 298K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97924 Å
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 3.1→37.5 Å / Num. obs: 38826

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
RefinementResolution: 3.1→37.5 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.857 / SU B: 64.529 / SU ML: 0.493 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.618 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.302 1726 5.1 %RANDOM
Rwork0.221 ---
obs0.225 33878 90.31 %-
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: 75.25 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20 Å24.35 Å2
2--0.99 Å20 Å2
3----1.38 Å2
Refinement stepCycle: LAST / Resolution: 3.1→37.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12522 0 94 27 12643
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02212984
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.94417664
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.84451534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.38624.646650
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.757152096
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5561552
X-RAY DIFFRACTIONr_chiral_restr0.0840.21858
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210052
X-RAY DIFFRACTIONr_nbd_refined0.2590.27047
X-RAY DIFFRACTIONr_nbtor_refined0.3220.28943
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2480
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.270.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3580.22
X-RAY DIFFRACTIONr_mcbond_it1.1871.57844
X-RAY DIFFRACTIONr_mcangle_it2.113212416
X-RAY DIFFRACTIONr_scbond_it1.44435993
X-RAY DIFFRACTIONr_scangle_it2.1734.55248
X-RAY DIFFRACTIONr_rigid_bond_restr1.258313837
X-RAY DIFFRACTIONr_sphericity_free4.538331
X-RAY DIFFRACTIONr_sphericity_bonded0.686312612
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1649LOOSE POSITIONAL0.35
1A1649LOOSE THERMAL1.9810
2A3215LOOSE POSITIONAL0.535
2A3215LOOSE THERMAL4.7110
3E1397LOOSE POSITIONAL0.165
3E1397LOOSE THERMAL0.8810
LS refinement shellResolution: 3.1→3.267 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.403 213 -
Rwork0.327 3859 -
all-4072 -
obs--75.3 %
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)
13.58854.47391.5717.91442.16646.1807-0.80190.0909-0.4537-0.0814-0.0914-0.6160.21310.49910.8934-0.1547-0.1160.1694-0.15250.1313-0.056545.7616-16.242112.6592
21.09760.4156-0.73962.8201-2.90265.15060.22140.19520.5411.3836-0.5029-0.4425-1.08890.62130.28150.2613-0.2284-0.18640.00460.18430.22250.40479.8853112.7647
36.5834-8.2592-7.044978.9163-22.280638.18531.00380.53091.17941.6035-1.5705-0.9063-2.11070.29340.56680.0570.0158-0.073-0.01770.11690.213252.057629.8117101.1157
42.96990.7878-1.72231.2491-0.89411.639-0.4946-0.1945-0.25560.0307-0.07-0.09870.3380.40390.56460.01140.14660.1723-0.00050.14810.030971.1196-1.97397.6453
53.85593.8506-2.405917.40493.47774.0512-0.02670.26160.3416-0.9159-0.0902-0.8128-0.31570.16480.1169-0.0829-0.0062-0.17010.0640.30120.182751.552510.145399.3885
63.11150.8418-1.74610.7202-0.70631.3262-0.41520.38470.0011-0.14980.1611-0.04320.3423-0.14660.2541-0.0598-0.00490.0228-0.05530.1-0.041562.15643.79790.8295
71.0016-0.595-1.471.79092.845.6354-0.34540.52250.0729-0.30020.2525-0.06460.5362-0.31650.09290.0355-0.23240.01410.29050.1777-0.159936.544738.168835.9196
81.0667-0.123-1.34221.10891.00083.9795-0.13960.4206-0.0105-0.27140.0291-0.1146-0.04480.25120.1105-0.3103-0.0323-0.048-0.10690.0675-0.158535.638940.061462.5712
94.8121-5.461411.496116.4458-20.247732.5237-1.1622-0.2099-0.54760.4111.04260.09050.60711.42340.1196-0.4210.11080.0407-0.1984-0.0471-0.048336.838130.177683.3021
100.3647-0.15730.3150.8933-0.68521.2297-0.0034-0.0452-0.0176-0.09490.20980.13060.0701-0.1598-0.2064-0.0904-0.0513-0.0098-0.11620.0343-0.079713.459329.478657.4247
111.40510.13080.58740.12831.252812.6117-0.39820.1282-0.3431-0.1928-0.0289-0.15020.82360.25940.4272-0.16230.1053-0.0395-0.02260.027-0.045633.845227.041263.9287
121.09020.3818-0.16720.646-0.5360.7964-0.01670.0421-0.1636-0.22420.1096-0.01110.2723-0.0367-0.0928-0.0157-0.0005-0.0152-0.04120-0.013222.018421.223261.6592
132.32280.4316-2.21663.9249-0.68983.34790.14640.1970.10570.10860.0640.1988-0.5115-0.4138-0.2104-0.02560.0346-0.0322-0.09730.0463-0.233723.2487-9.3436125.6754
142.69620.82661.00181.22660.16783.1005-0.09520.45970.0807-0.1346-0.1214-0.17470.01260.26010.2166-0.1377-0.05080.08110.11850.2935-0.012960.8649.735239.138
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA19 - 1021 - 84
2X-RAY DIFFRACTION1AE6161
3X-RAY DIFFRACTION1AK9011
4X-RAY DIFFRACTION2AA290 - 397272 - 379
5X-RAY DIFFRACTION2AL9021
6X-RAY DIFFRACTION3AA417 - 430399 - 412
7X-RAY DIFFRACTION4AA103 - 28985 - 271
8X-RAY DIFFRACTION5AA398 - 416380 - 398
9X-RAY DIFFRACTION6AA431 - 615413 - 597
10X-RAY DIFFRACTION6AA546 - 548528 - 530
11X-RAY DIFFRACTION7BB19 - 1021 - 84
12X-RAY DIFFRACTION7BM9011
13X-RAY DIFFRACTION7BN9021
14X-RAY DIFFRACTION8BB290 - 397272 - 379
15X-RAY DIFFRACTION8BB322304
16X-RAY DIFFRACTION9BB417 - 430399 - 412
17X-RAY DIFFRACTION10BB103 - 28985 - 271
18X-RAY DIFFRACTION11BB398 - 416380 - 398
19X-RAY DIFFRACTION12BB431 - 615413 - 597
20X-RAY DIFFRACTION12BG - H617 - 6181
21X-RAY DIFFRACTION13EC324 - 5021 - 179
22X-RAY DIFFRACTION13EI911
23X-RAY DIFFRACTION14FD324 - 5021 - 179
24X-RAY DIFFRACTION14FJ911

+
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