[English] 日本語
Yorodumi
- PDB-4adg: Crystal structure of the Rubella virus envelope Glycoprotein E1 i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4adg
TitleCrystal structure of the Rubella virus envelope Glycoprotein E1 in post-fusion form (crystal form II)
ComponentsE1 ENVELOPE GLYCOPROTEIN
KeywordsVIRAL PROTEIN / MEMBRANE FUSION
Function / homology
Function and homology information


T=4 icosahedral viral capsid / host cell Golgi membrane / host cell mitochondrion / clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / RNA binding ...T=4 icosahedral viral capsid / host cell Golgi membrane / host cell mitochondrion / clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / RNA binding / membrane / metal ion binding
Similarity search - Function
Rubella membrane glycoprotein E1, domain 3 / Rubella membrane glycoprotein E1, domain 1 / Rubella membrane glycoprotein E1, domain 2 / Rubella capsid / Rubella membrane glycoprotein E1 / Rubella membrane glycoprotein E2 / Rubella membrane glycoprotein E1, domain 2 / Rubella membrane glycoprotein E1, domain 3 / Rubella membrane glycoprotein E1, domain 1 / Rubella capsid domain superfamily ...Rubella membrane glycoprotein E1, domain 3 / Rubella membrane glycoprotein E1, domain 1 / Rubella membrane glycoprotein E1, domain 2 / Rubella capsid / Rubella membrane glycoprotein E1 / Rubella membrane glycoprotein E2 / Rubella membrane glycoprotein E1, domain 2 / Rubella membrane glycoprotein E1, domain 3 / Rubella membrane glycoprotein E1, domain 1 / Rubella capsid domain superfamily / Rubella membrane glycoprotein E1 / Rubella membrane glycoprotein E2 / Rubella capsid protein / Viral Envelope Glycoprotein; domain 2 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 2-acetamido-2-deoxy-beta-D-galactopyranose / DI(HYDROXYETHYL)ETHER / Structural polyprotein
Similarity search - Component
Biological speciesRUBELLA VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsDuBois, R.M. / Vaney, M.C. / Tortorici, M.A. / Al Kurdi, R. / Barba-Spaeth, G. / Rey, F.A.
Citation
Journal: Nature / Year: 2013
Title: Functional and Evolutionary Insight from the Crystal Structure of Rubella Virus Protein E1.
Authors: Dubois, R.M. / Vaney, M.C. / Tortorici, M.A. / Kurdi, R.A. / Barba-Spaeth, G. / Krey, T. / Rey, F.A.
#1: Journal: Nature / Year: 2004
Title: Conformational Change and Protein-Protein Interactions of the Fusion Protein of Semliki Forest Virus.
Authors: Gibbons, D.L. / Vaney, M. / Roussel, A. / Vigouroux, A. / Reilly, B. / Lepault, J. / Kielian, M. / Rey, F.A.
#2: Journal: Cell(Cambridge,Mass.) / Year: 2001
Title: The Fusion Glycoprotein Shell of Semliki Forest Virus: An Icosahedral Assembly Primed for Fusogenic Activation at Endosomal Ph.
Authors: Lescar, J. / Roussel, A. / Wien, M.W. / Navaza, J. / Fuller, S.D. / Wengler, G. / Wengler, G. / Rey, F.A.
#3: Journal: Structure / Year: 2006
Title: Structure and Interactions at the Viral Surface of the Envelope Protein E1 of Semliki Forest Virus.
Authors: Roussel, A. / Lescar, J. / Vaney, M. / Wengler, G. / Wengler, G. / Rey, F.A.
#4: Journal: Embo J. / Year: 2004
Title: Structure of a Flavivirus Envelope Glycoprotein in its Low-Ph-Induced Membrane Fusion Conformation.
Authors: Bressanelli, S. / Stiasny, K. / Allison, S.L. / Stura, E.A. / Duquerroy, S. / Lescar, J. / Heinz, F.X. / Rey, F.A.
History
DepositionDec 26, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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.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.value / _struct_conn.conn_type_id / _struct_conn.id / _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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E1 ENVELOPE GLYCOPROTEIN
B: E1 ENVELOPE GLYCOPROTEIN
C: E1 ENVELOPE GLYCOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,37028
Polymers151,7203
Non-polymers2,65025
Water20,7351151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23660 Å2
ΔGint-97.4 kcal/mol
Surface area49590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.680, 126.550, 130.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein E1 ENVELOPE GLYCOPROTEIN / SPIKE GLYCOPROTEIN E1


Mass: 50573.352 Da / Num. of mol.: 3 / Fragment: ECTODOMAIN, UNP RESIDUES 583-1017
Source method: isolated from a genetically manipulated source
Details: POLYPROTEIN FRAGMENT / Source: (gene. exp.) RUBELLA VIRUS / Strain: M33 / Plasmid: PMT MODIFIED INVITROGEN / Cell line (production host): SCHNEIDER 2 / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: P08563

-
Sugars , 2 types, 5 molecules

#2: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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
#7: Sugar ChemComp-NGA / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-acetyl-beta-D-galactosamine / 2-acetamido-2-deoxy-beta-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-D-GALACTOSAMINE / N-Acetylgalactosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-galactopyranosamineCOMMON NAMEGMML 1.0
b-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 6 types, 1171 molecules

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


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1151 / Source method: isolated from a natural source / Formula: H2O

-
Details

Nonpolymer detailsCHLORIDE ION (CL): THIS CHLORIDE ION IS LOCATED ON THE PSEUDO 3-FOLD AXIS OF THE E1 TRIMER. CALCIUM ...CHLORIDE ION (CL): THIS CHLORIDE ION IS LOCATED ON THE PSEUDO 3-FOLD AXIS OF THE E1 TRIMER. CALCIUM ION (CA): THE CALCIUM IONS ARE BONDED TO RESIDUES AT THE FUSION LOOPS. GLYCEROL (GOL): E1 PROTEIN WAS CRYSTALLIZED IN PRESENCE OF HIGH CONCENTRATION OF GLYCEROL. N-ACETYL-D-GALACTOSAMINE (NGA): THE THR RESIDUES 429 AND 430 ARE O-GLYCOSYLATED. ACETATE ION (ACT): ACETATE IONS ARE BONDED TO CALCIUM IONS AT THE FUSION LOOPS. N-ACETYL-D-GLUCOSAMINE (NAG): THE ASN RESIDUES 76 AND 177 ARE N-GLYCOSYLATED.
Sequence detailsECTODOMAIN OF E1 FROM AMINO ACIDS FROM 1 (583 IN POLYPROTEIN) TO 436 (1018 IN POLYPROTEIN) WITH THE ...ECTODOMAIN OF E1 FROM AMINO ACIDS FROM 1 (583 IN POLYPROTEIN) TO 436 (1018 IN POLYPROTEIN) WITH THE FOLLOWING SEQUENCE AT THE C-TERMINAL FEDDDDKAGWSHPQFEKGGGSGGGSGGGSWSHPQFEK

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59 % / Description: NONE
Crystal growDetails: 2-3% PEG4000, 100MM HEPES PH 7.5-8.0, 30% GLYCEROL. E1 PROTEIN WAS SOAKED WITH 25MM OF GALACTOSE 3-SULFATE (GAL3S, HEAD GROUP OF SULFATIDE) DURING ONE WEEK.

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.008
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 23, 2008 / Details: DYNAMICALLY BENDABLE
RadiationMonochromator: DOUBLE-CRYSTAL FIXED-EXIT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.18→45.34 Å / Num. obs: 104002 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 12.4 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 19.5
Reflection shellResolution: 2.18→2.3 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.4 / % possible all: 97.4

-
Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AD1

4ad1


Resolution: 2.18→20 Å / Cor.coef. Fo:Fc: 0.9449 / Cor.coef. Fo:Fc free: 0.9335 / Cross valid method: THROUGHOUT / σ(F): 0
Details: DISORDERED REGIONS 210-212 WERE NOT MODELED FOR THE A,B,C CHAINS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1934 5179 4.99 %RANDOM
Rwork0.1779 ---
obs0.1786 103791 98.94 %-
Displacement parametersBiso mean: 29.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.3616 Å20 Å20 Å2
2---0.1819 Å20 Å2
3---0.5435 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.18→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9717 0 165 1151 11033
LS refinement shellResolution: 2.18→2.24 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2259 360 4.91 %
Rwork0.2117 6970 -
all0.2124 7330 -
obs--98.94 %
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)
11.9488-0.68890.09622.6301-0.16341.22320.0156-0.0473-0.01090.0133-0.0116-0.10870.13070.2283-0.004-0.05520.0296-0.008-0.0167-0.0053-0.055640.7208-38.4583-28.9434
21.55410.2599-0.03691.1384-0.01671.87110.01930.13340.0933-0.2136-0.0603-0.144-0.00510.10270.041-0.0293-0.00730.0582-0.02370.0205-0.034540.3301-22.2454-43.9921
31.8799-0.31490.00782.29050.51292.03010.00450.1979-0.1772-0.05680.02960.05680.11770.009-0.034-0.0383-0.0240.0007-0.0399-0.0328-0.046125.1616-38.4501-44.6504
40.8974-0.3182-0.72570.43090.56421.0970.0288-0.15980.08880.03520.0041-0.01190.01110.0892-0.0329-0.0478-0.0181-0.0075-0.0168-0.0022-0.04888.7605-11.1445.4952
50.4616-0.5126-0.38750.80540.42760.62090.0373-0.00510.0647-0.06320.0051-0.0819-0.1587-0.0102-0.0425-0.0046-0.0181-0.0089-0.0522-0.0023-0.04019.29788.9108-11.8889
60.792-0.343-0.40780.34910.12660.5035-0.02940.0175-0.07180.04450.03230.09240.0353-0.0568-0.0029-0.0455-0.0130.0063-0.04650.0179-0.009-9.5445-10.001-13.9325
72.5379-0.0642-1.43640.69470.04461.8168-0.01130.04270.1492-0.06580.0784-0.2204-0.00590.1975-0.0671-0.1022-0.04210.0060.0298-0.02080.006147.8681-10.7818-23.5872
80.68280.019-0.14512.06851.6912.93340.0260.0988-0.0472-0.2429-0.01360.0103-0.0769-0.0479-0.01250.0189-0.0031-0.012-0.03460.0154-0.073912.4206-18.6377-51.9358
92.5061-1.93610.05733.569-0.24941.0119-0.02610.0533-0.12030.0354-0.04750.0310.14510.10520.0736-0.02030.0079-0.0024-0.06890.03-0.020620.9918-47.5364-17.4306
100.8048-0.0097-1.18440.05561.17290.08170.0057-0.009-0.0327-0.0490.00770.01620.05990.0117-0.01330.0078-0.0172-0.00960.0565-0.0150.025555.7541-24.9522-35.1689
110.0671-1.5774-0.41440.0804-0.08470.67040.0005-0.0063-0.0463-0.0223-0.0112-0.0599-0.01120.01390.01060.05160.00280.0150.0425-0.00110.004628.0855-29.1809-59.6775
120.0372-0.3899-1.17350.14520.44930.0546-0.00010.0352-0.0115-0.0122-0.0016-0.00820.00290.02940.00160.0433-0.01950.00970.01310.0110.059532.6318-54.1012-32.5009
130.4856-0.45930.364200.329700.00050.04580.0460.00620.01870.0114-0.06750.0338-0.0191-0.0197-0.02720.0417-0.0461-0.01370.020123.16166.3079-8.8742
140-0.23880.01440-0.64930.53390.0039-0.0219-0.0367-0.0244-0.00050.05330.0432-0.1147-0.0034-0.0328-0.0254-0.00410.0131-0.05240.0053-6.6118-6.0163-27.6712
1500.6195-0.15340.43880.012300.009-0.05130.02560.0469-0.01370.01170.02680.02160.00470.00690.04450.0063-0.00230.0237-0.01956.1693-24.98221.9172
160.01760.02250.000300.02990.0236-0.0005-0.00420.00120.0069-0.00140.0009-0.00280.00030.00190.0057-0.0102-0.02510.035-0.0229-0.008247.9119-31.649-20.4044
170.00970.00840.01140.0057-0.00640.0005-0.00010.0005-0.0001-0.00010.0008-0.00250.00020.0023-0.00060.00750.0041-0.00810.00660.00290.025216.731418.9661-10.3111
180.0044-0.0064-0.01040.0186-0.00580.0282-0.0002-0.00150.0045-0.00040.00060.0016-0.004-0.0013-0.00040.03260.00430.00720.00260.0207-0.001533.1794-13.9538-51.2512
190.0220.0136-0.0040.0242-0.00010.00010.0005-0.0021-0.0001-0.0007-0.00030.0049-0.0002-0.0058-0.00020.0008-0.02030.00280.00180.00690.037917.1351-46.3865-37.941
2000.00990.01780.01220.00070.00430-0.0024-0.00120.0010-0.00050.00110.00020.00010.0131-0.0263-0.015-0.00090.00570.0151-16.0396-24.1843-9.4742
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1:30, 163:200, 318:327)
2X-RAY DIFFRACTION2CHAIN B AND (RESID 1:30, 163:200, 318:327)
3X-RAY DIFFRACTION3CHAIN C AND (RESID 1:30, 163:200, 318:327)
4X-RAY DIFFRACTION4CHAIN A AND (RESID 31:162)
5X-RAY DIFFRACTION5CHAIN B AND (RESID 31:162)
6X-RAY DIFFRACTION6CHAIN C AND (RESID 31:162)
7X-RAY DIFFRACTION7CHAIN A AND (RESID 342:413)
8X-RAY DIFFRACTION8CHAIN B AND (RESID 342:413)
9X-RAY DIFFRACTION9CHAIN C AND (RESID 342:413)
10X-RAY DIFFRACTION10CHAIN A AND (RESID 328:341)
11X-RAY DIFFRACTION11CHAIN B AND (RESID 328:341)
12X-RAY DIFFRACTION12CHAIN C AND (RESID 328:341)
13X-RAY DIFFRACTION13CHAIN A AND (RESID 414:435)
14X-RAY DIFFRACTION14CHAIN B AND (RESID 414:435)
15X-RAY DIFFRACTION15CHAIN C AND (RESID 414:435)
16X-RAY DIFFRACTION16CHAIN A AND RESID 1001
17X-RAY DIFFRACTION17CHAIN A AND RESID 4001
18X-RAY DIFFRACTION18CHAIN B AND RESID 1001
19X-RAY DIFFRACTION19CHAIN C AND RESID 1001
20X-RAY DIFFRACTION20CHAIN C AND RESID 2001

+
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