[English] 日本語
Yorodumi
- PDB-6dc5: RSV prefusion F in complex with AM22 Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dc5
TitleRSV prefusion F in complex with AM22 Fab
Components
  • Fab AM22 heavy chain
  • Fab AM22 light chain
  • RSV fusion glycoprotein
KeywordsIMMUNE SYSTEM / Viral fusion glycoprotein / human antibody
Function / homology
Function and homology information


symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope ...symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / extracellular region / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Fibritin C-terminal / Fibritin C-terminal region / : / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site ...Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Fibritin C-terminal / Fibritin C-terminal region / : / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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 / Mainly Beta
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / Envelope glycoprotein / Fusion glycoprotein F0 / IGH@ protein / Ig-like domain-containing protein
Similarity search - Component
Biological speciesHuman respiratory syncytial virus A
Human immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsJones, H.G. / McLellan, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM113132 United States
CitationJournal: Plos Pathog. / Year: 2019
Title: Alternative conformations of a major antigenic site on RSV F.
Authors: Jones, H.G. / Battles, M.B. / Lin, C.C. / Bianchi, S. / Corti, D. / McLellan, J.S.
History
DepositionMay 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RSV fusion glycoprotein
D: RSV fusion glycoprotein
G: RSV fusion glycoprotein
B: Fab AM22 heavy chain
C: Fab AM22 light chain
E: Fab AM22 heavy chain
F: Fab AM22 light chain
H: Fab AM22 heavy chain
I: Fab AM22 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)333,48421
Polymers331,8469
Non-polymers1,63812
Water00
1
A: RSV fusion glycoprotein
B: Fab AM22 heavy chain
C: Fab AM22 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,1617
Polymers110,6153
Non-polymers5464
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: RSV fusion glycoprotein
E: Fab AM22 heavy chain
F: Fab AM22 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,1617
Polymers110,6153
Non-polymers5464
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: RSV fusion glycoprotein
H: Fab AM22 heavy chain
I: Fab AM22 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,1617
Polymers110,6153
Non-polymers5464
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.450, 152.180, 202.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

-
Components

-
Antibody , 2 types, 6 molecules BEHCFI

#2: Antibody Fab AM22 heavy chain


Mass: 24123.217 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGH@ / Production host: Homo sapiens (human) / References: UniProt: Q6GMX6
#3: Antibody Fab AM22 light chain


Mass: 23273.938 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: Q8TCD0

-
Protein / Sugars , 2 types, 6 molecules ADG

#1: Protein RSV fusion glycoprotein / Protein F


Mass: 63218.344 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A (strain A2), (gene. exp.) Human immunodeficiency virus 1
Strain: A2 / Production host: Homo sapiens (human) / References: UniProt: P03420, UniProt: M1E1E4
#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.: 3
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 , 2 types, 9 molecules

#5: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 32% PEG 400, 4% PEG 3350, 0.01 M cadmium chloride, 0.1 M sodium acetate pH 5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→50.55 Å / Num. obs: 52333 / % possible obs: 99.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 58.62 Å2 / CC1/2: 0.933 / Net I/σ(I): 5.7
Reflection shellResolution: 3.5→3.61 Å / Rmerge(I) obs: 0.903 / Mean I/σ(I) obs: 2 / Num. unique obs: 4425 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MMS, 6DC4

4mms

6dc4


Resolution: 3.5→47.231 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / Phase error: 24.93
RfactorNum. reflection% reflection
Rfree0.2801 2606 4.98 %
Rwork0.2172 --
obs-52294 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 211.52 Å2 / Biso min: 3.96 Å2
Refinement stepCycle: final / Resolution: 3.5→47.231 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20199 0 86 0 20285
Biso mean--40.7 --
Num. residues----2644
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.56360.3171530.2992532X-RAY DIFFRACTION98
3.5636-3.63220.36051260.28862543X-RAY DIFFRACTION99
3.6322-3.70630.36371360.29252586X-RAY DIFFRACTION99
3.7063-3.78680.38021190.29152601X-RAY DIFFRACTION100
3.7868-3.87490.36251130.26852589X-RAY DIFFRACTION100
3.8749-3.97170.30361560.26282600X-RAY DIFFRACTION100
3.9717-4.07910.31421390.25322548X-RAY DIFFRACTION100
4.0791-4.1990.29791550.2282602X-RAY DIFFRACTION100
4.199-4.33450.28531360.21842591X-RAY DIFFRACTION100
4.3345-4.48930.26311520.20942591X-RAY DIFFRACTION100
4.4893-4.66890.27081340.19542585X-RAY DIFFRACTION100
4.6689-4.88110.23881370.18132616X-RAY DIFFRACTION100
4.8811-5.13820.24811340.18432618X-RAY DIFFRACTION100
5.1382-5.45970.23481440.19532638X-RAY DIFFRACTION100
5.4597-5.88050.22061150.19932638X-RAY DIFFRACTION100
5.8805-6.47090.26781370.18772635X-RAY DIFFRACTION100
6.4709-7.40420.26661440.19982659X-RAY DIFFRACTION100
7.4042-9.31680.23651260.16142712X-RAY DIFFRACTION100
9.3168-47.230.24031500.17662804X-RAY DIFFRACTION100
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)
12.03271.0555-0.00781.504-0.19070.0377-0.0589-0.33250.52220.10860.0982-0.3363-0.47890.1566-0.00461.3415-0.0815-0.00220.4216-0.21190.8597-45.774496.388-47.695
26.3266-1.5976-0.49274.62321.39112.2575-0.3341-0.20760.0913-0.34310.2863-0.0906-0.4821-0.06280.0110.6358-0.0180.22451.04110.05030.4566-65.528449.2481-33.731
32.13672.66620.61364.5628-1.22093.3668-0.029-0.1269-0.19210.4207-0.00980.5908-0.4626-0.09650.05310.27420.08770.14740.46110.05680.3332-61.013860.1463-33.4903
40.2983-0.66360.08783.96140.17580.65290.0022-0.15730.0961-0.72350.12550.5079-0.477-0.3718-0.05990.50980.20330.07770.37920.04140.5411-62.750569.3234-45.3252
51.22040.7741-0.08562.85810.07560.8327-0.1427-0.16460.4808-0.13070.1912-0.1222-0.43960.1098-0.03470.94680.186-0.01310.2289-0.21550.5184-49.537291.4059-44.4553
60.24170.13840.07840.1398-0.03370.1194-0.0809-0.27850.7194-0.03840.0977-0.2187-0.6686-0.0756-0.07411.6998-0.0019-0.23450.4738-0.34891.5062-35.6084111.7512-36.9838
72.04430.5763-0.64050.406-0.26840.43470.0720.27990.2142-0.08920.27580.5230.0045-0.4089-0.01730.0995-0.11840.00060.61030.39360.8115-81.730330.6306-43.3663
82.51680.59640.56451.06340.47072.46810.0712-0.248-0.05170.19650.01410.0450.2118-0.179-0.04150.0596-0.05250.04280.29990.08520.5609-85.9045-0.5577-23.8962
91.36740.6159-0.69371.012-0.1370.73160.06110.116-0.0335-0.17170.2298-0.044-0.0069-0.1461-0.0360.057-0.12860.02520.38120.19980.372-61.710924.0698-40.245
102.1040.48080.68511.47760.62261.40450.05780.4527-0.28120.00420.0972-0.0585-0.0070.1557-0.12280.08680.03870.03740.39670.05620.5208-75.0568-6.9288-34.4131
115.7758-0.3977-2.55090.1171-0.07925.5863-0.1735-0.36380.8772-0.0135-0.07350.6581-0.5805-0.14780.22640.99480.4387-0.10180.7049-0.25740.7707-74.9712102.5069-29.7472
120.78050.0985-0.30451.36730.07880.1225-0.3791-0.3925-0.01140.20980.1444-0.2662-0.6258-0.35660.17850.84110.5385-0.07461.072-0.00160.5171-52.639472.2963-16.2443
134.4423-0.52720.49924.8465-1.07883.22090.1733-0.20490.05680.22680.2111-0.1869-0.4302-0.0392-0.35280.15820.06510.06450.337-0.05990.2657-33.708256.724-26.0336
140.2279-0.0643-0.15981.68371.20910.9136-0.2104-0.2945-0.04870.2487-0.10640.4447-0.3171-0.42570.13020.98080.46460.31531.2161-0.09840.543-49.1868.8628-9.6961
150.4555-0.24830.32010.159-0.170.224-0.4616-0.77570.37670.20740.3040.0085-0.6108-0.4464-0.00760.9970.69260.05141.0014-0.3450.6747-60.851888.9432-27.3512
161.83520.37410.92840.3356-0.54592.551-0.1050.0885-0.1888-0.1857-0.1777-0.52450.10530.21180.23731.66020.5118-0.42651.1721-0.71162.0852-59.9691126.8799-21.6761
172.3684-1.13151.25721.5005-1.05841.7638-0.2167-0.40230.04580.28850.22090.0983-0.0280.03940.01180.17480.08510.05960.52580.14380.2558-24.266325.347-13.1357
184.3895-0.0392-0.32882.7886-0.31592.4705-0.07210.056-0.12550.05230.1719-0.3136-0.00870.0872-0.02040.2320.1694-0.04560.52480.12810.33771.97143.527-27.6937
191.6318-0.741-0.20581.7630.27991.46840.042-0.5951-0.122-0.11970.10610.08630.1136-0.068-0.09610.1425-0.0082-0.06530.3630.15350.3146-29.93423.8073-33.5071
200.9283-1.47710.96033.1704-2.26843.09410.2331-0.113-0.2055-0.12590.07080.54010.1859-0.2344-0.27430.17090.0073-0.05190.4870.0580.5286-11.5762-3.7073-33.9361
210.23030.1226-0.0970.08230.02850.2293-0.1696-0.53280.33910.51790.10940.2677-0.4271-0.2528-0.03731.17830.33750.05590.88-0.57790.9544-31.652490.0116-18.607
221.8-2.4666-1.9276.7462-1.76619.6046-0.3649-0.33931.32720.4519-0.1694-0.0217-1.05150.15060.4940.7670.0065-0.07670.5371-0.05790.5998-38.384259.1849-60.4465
233.5495-0.6210.04941.59320.63282.0039-0.12720.20380.3583-0.40160.2710.7056-0.6173-0.3029-0.06360.34150.0388-0.02070.24590.12430.3642-41.491863.7637-51.5952
240.27830.47380.31391.15860.18350.6127-0.058-0.12950.15410.00560.0202-0.5498-0.60590.2441-0.09840.5661-0.17290.13060.3335-0.28791.0196-25.412175.9387-44.4305
250.8438-0.2379-0.13982.7030.77660.685-0.1772-0.74420.39650.39640.2846-0.6015-0.42030.0298-0.20480.5920.1319-0.0450.5646-0.3110.7657-31.986176.3465-32.4169
260.3965-0.1635-0.1450.15430.23690.3799-0.1141-0.24210.4757-0.11520.00330.0328-0.4082-0.2322-0.14151.51940.6954-0.33831.4547-0.94341.0657-44.5262104.3638-8.4211
270.1013-0.1634-0.18110.33160.15110.8563-0.08090.08420.1109-0.27330.1898-0.4457-0.31180.3596-0.14370.4329-0.34530.22150.3444-0.12380.3617-26.575640.8971-76.131
285.27250.0088-0.55183.56150.19243.1260.28010.37420.1338-0.78410.020.1903-0.56330.259-0.23120.5513-0.0832-0.08370.26540.01710.2918-45.303218.354-99.7443
291.81480.31920.22552.14620.10252.21420.149-0.0138-0.06150.2884-0.06870.0842-0.15450.2383-0.09590.151-0.11690.00910.17160.04030.2572-40.228531.0464-63.4771
302.8358-0.4915-1.25482.03471.05372.41120.1743-0.0855-0.3186-0.1318-0.0334-0.0777-0.0960.0232-0.13720.1348-0.0999-0.10050.28450.02520.2275-41.96458.0595-87.4931
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 27:62)A27 - 62
2X-RAY DIFFRACTION2(chain A and resid 63:73)A63 - 73
3X-RAY DIFFRACTION3(chain A and resid 74:98)A74 - 98
4X-RAY DIFFRACTION4(chain A and resid 137:234)A137 - 234
5X-RAY DIFFRACTION5(chain A and resid 235:348)A235 - 348
6X-RAY DIFFRACTION6(chain A and resid 349:509)A349 - 509
7X-RAY DIFFRACTION7(chain B and resid 1:111)B1 - 111
8X-RAY DIFFRACTION8(chain B and resid 112:215)B112 - 215
9X-RAY DIFFRACTION9(chain C and resid 1:105)C1 - 105
10X-RAY DIFFRACTION10(chain C and resid 106:212)C106 - 212
11X-RAY DIFFRACTION11(chain D and resid 26:41)D26 - 41
12X-RAY DIFFRACTION12(chain D and resid 42:67)D42 - 67
13X-RAY DIFFRACTION13(chain D and resid 68:98)D68 - 98
14X-RAY DIFFRACTION14(chain D and resid 137:202)D137 - 202
15X-RAY DIFFRACTION15(chain D and resid 203:475)D203 - 475
16X-RAY DIFFRACTION16(chain D and resid 476:511)D476 - 511
17X-RAY DIFFRACTION17(chain E and resid 1:111)E1 - 111
18X-RAY DIFFRACTION18(chain E and resid 112:215)E112 - 215
19X-RAY DIFFRACTION19(chain F and resid 1:105)F1 - 105
20X-RAY DIFFRACTION20(chain F and resid 106:211)F106 - 211
21X-RAY DIFFRACTION21(chain G and resid 27:62)G27 - 62
22X-RAY DIFFRACTION22(chain G and resid 63:71)G63 - 71
23X-RAY DIFFRACTION23(chain G and resid 72:97)G72 - 97
24X-RAY DIFFRACTION24(chain G and resid 137:210)G137 - 210
25X-RAY DIFFRACTION25(chain G and resid 211:322)G211 - 322
26X-RAY DIFFRACTION26(chain G and resid 323:509)G323 - 509
27X-RAY DIFFRACTION27(chain H and resid 1:111)H1 - 111
28X-RAY DIFFRACTION28(chain H and resid 112:216)H112 - 216
29X-RAY DIFFRACTION29(chain I and resid 1:105)I1 - 105
30X-RAY DIFFRACTION30(chain I and resid 106:214)I106 - 214

+
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