[English] 日本語
Yorodumi
- PDB-7nxc: Crystal structure of the receptor binding domain of SARS-CoV-2 P.... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7nxc
TitleCrystal structure of the receptor binding domain of SARS-CoV-2 P.1 variant Spike glycoprotein in complex with ACE2
Components
  • Processed angiotensin-converting enzyme 2
  • Spike protein S1
KeywordsVIRAL PROTEIN/HYDROLASE / SARS-CoV-2 B.1.1.7 variant / B.1.351 variant / P.1 variant / antibody / receptor-binding-domain / spike / neutralisation / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN / HYDROLASE / VIRAL PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


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 / regulation of systemic arterial blood pressure by renin-angiotensin / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / regulation of vasoconstriction ...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 / regulation of systemic arterial blood pressure by renin-angiotensin / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / regulation of vasoconstriction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / negative regulation of signaling receptor activity / receptor-mediated endocytosis of virus by host cell / carboxypeptidase activity / Attachment and Entry / viral life cycle / positive regulation of cardiac muscle contraction / regulation of cytokine production / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / regulation of transmembrane transporter activity / brush border membrane / negative regulation of ERK1 and ERK2 cascade / cilium / positive regulation of reactive oxygen species metabolic process / metallopeptidase activity / endocytic vesicle membrane / regulation of cell population proliferation / virus receptor activity / regulation of inflammatory response / endopeptidase activity / Maturation of spike protein / viral translation / Translation of Structural Proteins / host cell surface / Virion Assembly and Release / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Potential therapeutics for SARS / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / apical plasma membrane / receptor ligand activity / membrane raft / endocytosis involved in viral entry into host cell / endoplasmic reticulum lumen / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / cell surface / extracellular space / extracellular exosome / zinc ion binding / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / Neutral zinc metallopeptidases, zinc-binding region signature. / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal ...Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / Neutral zinc metallopeptidases, zinc-binding region signature. / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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 / 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 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
Similarity search - Domain/homology
Spike glycoprotein / Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.14 Å
AuthorsZhou, D. / Ren, J. / Stuart, D.
Funding support United Kingdom, China, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 United Kingdom
CAMS Innovation Fund for Medical Sciences (CIFMS)2018-I2M-2-002 China
Citation
Journal: Cell / Year: 2021
Title: Antibody evasion by the P.1 strain of SARS-CoV-2.
Authors: Dejnirattisai, W. / Zhou, D. / Supasa, P. / Liu, C. / Mentzer, A.J. / Ginn, H.M. / Zhao, Y. / Duyvesteyn, H.M.E. / Tuekprakhon, A. / Nutalai, R. / Wang, B. / Lopez-Camacho, C. / Slon-Campos, ...Authors: Dejnirattisai, W. / Zhou, D. / Supasa, P. / Liu, C. / Mentzer, A.J. / Ginn, H.M. / Zhao, Y. / Duyvesteyn, H.M.E. / Tuekprakhon, A. / Nutalai, R. / Wang, B. / Lopez-Camacho, C. / Slon-Campos, J. / Walter, T.S. / Skelly, D. / Costa Clemens, S.A. / Naveca, F.G. / Nascimento, V. / Nascimento, F. / Fernandes da Costa, C. / Resende, P.C. / Pauvolid-Correa, A. / Siqueira, M.M. / Dold, C. / Levin, R. / Dong, T. / Pollard, A.J. / Knight, J.C. / Crook, D. / Lambe, T. / Clutterbuck, E. / Bibi, S. / Flaxman, A. / Bittaye, M. / Belij-Rammerstorfer, S. / Gilbert, S.C. / Carroll, M.W. / Klenerman, P. / Barnes, E. / Dunachie, S.J. / Paterson, N.G. / Williams, M.A. / Hall, D.R. / Hulswit, R.J.G. / Bowden, T.A. / Fry, E.E. / Mongkolsapaya, J. / Ren, J. / Stuart, D.I. / Screaton, G.R.
#1: Journal: Biorxiv / Year: 2021
Title: Antibody evasion by the Brazilian P.1 strain of SARS-CoV-2
Authors: Dejnirattisai, W. / Zhou, D. / Supasa, P. / Liu, C. / Mentzer, A.J. / Ginn, H.M. / Zhao, Y. / Duyvesteyn, H.M. / Tuekprakhon, A. / Nutalai, R. / Wang, B. / Paesen, G.C. / Lopez-Camacho, C. / ...Authors: Dejnirattisai, W. / Zhou, D. / Supasa, P. / Liu, C. / Mentzer, A.J. / Ginn, H.M. / Zhao, Y. / Duyvesteyn, H.M. / Tuekprakhon, A. / Nutalai, R. / Wang, B. / Paesen, G.C. / Lopez-Camacho, C. / Slon-Campos, J. / Walter, T.S. / Skelly, D. / Clemens, S.A.C. / Naveca, F.G. / Nascimento, V. / Nascimento, F. / Dold, C. / Levin, R. / Dong, T. / Pollard, A.J. / Knight, J.C. / Crook, D. / Lambe, T. / Clutterbuck, E. / Bibi, S. / Flaxman, A. / Bittaye, M. / Belij-Rammerstorfer, S. / Gilbert, S. / Carroll, M.W. / Klenerman, P. / Barnes, E. / Dunachie, S.J. / Paterson, N.G. / Williams, M.A. / Hall, D.R. / Hulswit, R.J.G. / Bowden, T.A. / Fry, E.E. / Mongkolsapaya, J. / Ren, J. / Stuart, D.I. / Screaton, G.R.
History
DepositionMar 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 9, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Processed angiotensin-converting enzyme 2
B: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4187
Polymers93,3122
Non-polymers1,1065
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint11 kcal/mol
Surface area34950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.502, 103.502, 225.907
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

#1: Protein Processed angiotensin-converting enzyme 2


Mass: 70139.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACE2, UNQ868/PRO1885 / Production host: Homo sapiens (human) / References: UniProt: Q9BYF1
#2: Protein Spike protein S1


Mass: 23171.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#3: 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.: 5 / Source method: obtained synthetically / 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
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 62.06 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Imidazole pH 7.0 and 20% w/v Polyethylene glycol 6,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3.14→70 Å / Num. obs: 22273 / % possible obs: 100 % / Redundancy: 25.7 % / Biso Wilson estimate: 87.49 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.5 / Rpim(I) all: 0.1 / Net I/σ(I): 5.3
Reflection shellResolution: 3.14→3.19 Å / Num. unique obs: 1047 / CC1/2: 0.31

-
Processing

Software
NameVersionClassification
GDA1.19_4092data collection
PHENIX1.19_4092refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LZG

6lzg


Resolution: 3.14→69.62 Å / SU ML: 0.4856 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.4576
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2783 1094 4.93 %
Rwork0.2263 21090 -
obs0.2287 22184 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 90.4 Å2
Refinement stepCycle: LAST / Resolution: 3.14→69.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6405 0 70 0 6475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036656
X-RAY DIFFRACTIONf_angle_d0.59539048
X-RAY DIFFRACTIONf_chiral_restr0.0433962
X-RAY DIFFRACTIONf_plane_restr0.00411166
X-RAY DIFFRACTIONf_dihedral_angle_d13.55152404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.14-3.280.36061340.37382531X-RAY DIFFRACTION99
3.28-3.460.33971630.32932574X-RAY DIFFRACTION99.85
3.46-3.670.31841380.2872569X-RAY DIFFRACTION99.89
3.67-3.960.29871350.24442615X-RAY DIFFRACTION100
3.96-4.350.29221090.22442635X-RAY DIFFRACTION99.85
4.35-4.980.25271360.19362635X-RAY DIFFRACTION100
4.98-6.280.28641300.21342692X-RAY DIFFRACTION100
6.28-69.620.22661490.17992839X-RAY DIFFRACTION99.83
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)
10.270208886261-0.4053213211690.1476831595640.8893944828830.5376372881271.812594636190.005848556338840.0831957728821-0.0439320453624-0.06939307060780.0880175861154-0.035741517308-0.281884770196-0.200090258779-0.0426372429410.6668298638250.04243153710010.07842273500420.9345641734820.01259986453850.82715680595-37.69653338729.4008058597-12.0849312481
21.84577959819-0.779447789567-0.4526464594031.43808841970.2053379745841.283820262060.05886451303850.200658659396-0.1519149419390.0847261057126-0.2830725855830.2745188434560.326374424298-0.2803294505710.0943474643540.618509377897-0.0604953945628-0.03947187109270.750530725515-0.07789520898950.600181652937-38.190998780311.4665291489-38.9629088126
31.02856643336-0.2410377844250.240282465411.608166130720.2824304322971.01814949027-0.0559101297662-0.04915894711270.0677279222826-0.02689162586930.05464667122790.0761399223768-0.1632223194940.16021571566-0.06543467905990.733260846479-0.07990695402410.02408975325870.826806548346-0.04734347723040.667392101583-17.582786934515.286369961-35.091666176
40.6356974227270.1569284744120.4980299147951.73194346719-0.06676778861611.522624632150.0216998947126-0.110367995033-0.1869264930260.201441787413-0.1801516164210.3706049753650.3208804061950.04422711172270.106071477750.8274534375470.03157771481820.07091410516820.9399315232590.004637920160040.771589513317-21.31445558695.6651979727-10.3921720928
51.68989473377-0.6071967686620.00877133227620.855174748684-0.2712370230450.981893986902-0.009159715194270.03273990454430.1569814809-0.0426191400489-0.0497135123964-0.113603865079-0.02955063020230.06411278983690.03739832021210.66066260534-0.05960764286180.04857036449230.694225512668-0.05477614425330.60862397335-16.162706569916.4712967595-31.2565596867
61.340822361740.1068988977411.297161997610.681182535050.5231248236881.53444206098-0.324744458457-0.933444013057-0.7871727691370.616718554040.132844714030.3460170573540.161316808136-0.12674607813-0.1829565086031.058233145590.1997182852870.1764690279671.227382614450.2593042876020.912000725429-34.159007167519.637440161631.7214105627
70.636101784652-1.203379761420.03236550701242.89847589873-0.351108215290.155491715646-0.0379436472425-0.586852952752-0.2070835268410.34529439083-0.106584962047-0.5568233067670.5876933527671.44646066949-0.02050986134560.8917173663820.1536384373760.08099102242821.43376661860.01732823307910.832814808975-24.581996017420.955679633927.5424970629
80.873116814341-0.610718573714-0.1773444331490.728673748819-0.5526021751281.81764216932-0.387981069945-0.265948316689-0.2089108617850.2854168134660.288939013224-0.1791090174360.1884440492670.9919843436940.007594676341940.8445147490840.07059954400130.01349829047881.08318761197-0.01097074360090.754464604065-26.736750491126.339649703720.2526471956
90.811211308404-0.288052813376-0.519501385721.5860377042-0.4841802302060.6318259977230.251214426828-0.0384226600505-0.5420159406860.02812877356230.0436891496801-0.242098897428-0.3730075262320.00677694898641-0.05175861703850.7718271161140.0422736548517-0.07218093501510.646938639873-0.1010318789740.6666773297-35.979736957531.71138107915.0224123634
102.476148032762.10275332015-0.2753825301181.912891697740.04942253904462.086800484330.0471040416546-0.300913080020.0130580076932-0.363622459065-0.2933179974180.261514803605-1.17416135638-0.0929797552034-0.0713282660941.051401305290.04057187717440.09499550175040.920064594944-0.1196220541180.787508042688-40.591550351143.01105063025.70868135228
115.372979843660.5219697449461.832495982082.037836339811.52924655597.182396327810.0129906056998-0.2123580295710.02603527249830.3375948937050.0004277157592940.5652248749970.0577048075479-0.33774869898-0.4934603323520.6289667075880.1375782837370.03296445392250.880174449078-0.09300916437670.994393979623-33.630729555817.79095918986.72600741713
121.684348017192.744221160080.08127711349556.65823850487-2.42201749983.498336114410.721407166333-0.8258013592480.4582543915152.29380046193-0.4149444342350.0457870601061-0.306887645380.262467782785-0.1951139975031.31801600720.0625869389805-0.028034903631.20569821832-0.1056540825331.21959440248-27.957531170924.561549422834.6676957443
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 19 through 129 )AA19 - 1291 - 111
22chain 'A' and (resid 130 through 193 )AA130 - 193112 - 175
33chain 'A' and (resid 194 through 293 )AA194 - 293176 - 275
44chain 'A' and (resid 294 through 431 )AA294 - 431276 - 413
55chain 'A' and (resid 432 through 614 )AA432 - 614414 - 596
66chain 'B' and (resid 333 through 370 )BF333 - 3701 - 38
77chain 'B' and (resid 371 through 409 )BF371 - 40939 - 77
88chain 'B' and (resid 410 through 442 )BF410 - 44278 - 110
99chain 'B' and (resid 443 through 469 )BF443 - 469111 - 137
1010chain 'B' and (resid 470 through 494 )BF470 - 494138 - 162
1111chain 'B' and (resid 495 through 506 )BF495 - 506163 - 174
1212chain 'B' and (resid 507 through 527 )BF507 - 527175 - 195

+
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