[English] 日本語
Yorodumi
- PDB-4b3v: Crystal structure of the Rubella virus glycoprotein E1 in its pos... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4b3v
TitleCrystal structure of the Rubella virus glycoprotein E1 in its post-fusion form crystallized in presence of 20mM of Calcium Acetate
ComponentsE1 ENVELOPE GLYCOPROTEIN
KeywordsVIRAL PROTEIN / ENVELOPE GLYCOPROTEIN / MEMBRANE FUSION
Function / homology
Function and homology information


T=4 icosahedral viral capsid / host cell Golgi membrane / host cell mitochondrion / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / 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 / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / RNA binding / metal ion binding / membrane
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: 1.98 Å
AuthorsVaney, M.C. / DuBois, R.M. / Tortorici, M.A. / 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: 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.
#2: 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.
#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
DepositionJul 26, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Mar 18, 2015Group: Database references
Revision 1.3Jun 14, 2017Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_vector_type
Revision 1.4Oct 16, 2019Group: Data collection / Derived calculations / Other / Category: pdbx_database_status / reflns_shell / struct_conn
Item: _pdbx_database_status.status_code_sf / _reflns_shell.Rmerge_I_obs / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / 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_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 1.6Dec 20, 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 1.7Oct 23, 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: E1 ENVELOPE GLYCOPROTEIN
B: E1 ENVELOPE GLYCOPROTEIN
C: E1 ENVELOPE GLYCOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,60440
Polymers151,7203
Non-polymers3,88437
Water20,3751131
1
A: E1 ENVELOPE GLYCOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,92514
Polymers50,5731
Non-polymers1,35113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: E1 ENVELOPE GLYCOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,61112
Polymers50,5731
Non-polymers1,03811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: E1 ENVELOPE GLYCOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,06814
Polymers50,5731
Non-polymers1,49413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.272, 126.163, 129.375
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 / ENVELOPE GLYCOPROTEIN E1


Mass: 50573.352 Da / Num. of mol.: 3 / Fragment: ECTODOMAIN, RESIDUES 583-1018
Source method: isolated from a genetically manipulated source
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, 6 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


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
#3: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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 , 7 types, 1162 molecules

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


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1131 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY
Nonpolymer detailsCALCIUM ION (CA): THE CALCIUM IONS ARE BONDED TO RESIDUES AT THE FUSION LOOPS OF THREE PROTOMERS. ...CALCIUM ION (CA): THE CALCIUM IONS ARE BONDED TO RESIDUES AT THE FUSION LOOPS OF THREE PROTOMERS. SODIUM ION (NA): THE SODIUM ION IS BONDED TO RESIDUES AT THE FUSION LOOPS OF ONE PROTOMER. GLYCEROL (GOL): E1 PROTEIN WAS CRYSTALLIZED IN PRESENCE OF HIGH CONCENTRATION OF GLYCEROL. N-ACETYL-D-GALACTOSAMINE (NGA): THE THR RESIDUE 430 IS O-GLYCOSILATED. N-ACETYL-D-GLUCOSAMINE (NAG): THE ASN RESIDUES 76 AND 177 ARE N-GLYCOSILATED.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59 % / Description: NONE
Crystal growDetails: 1-6% PEG 4K, 100 MM NAHEPES PH 8, 25% GLYCEROL, 20 MM CA(OAC)2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 2, 2010 / Details: DYNAMICALLY BENDABLE
RadiationMonochromator: DOUBLE-CRYSTAL FIXED-EXIT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→43.72 Å / Num. obs: 135009 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 29.81 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.1
Reflection shellResolution: 1.98→2.08 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2 / % possible all: 81.5

-
Processing

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

4adi


Resolution: 1.98→28.99 Å / Cor.coef. Fo:Fc: 0.9503 / Cor.coef. Fo:Fc free: 0.946 / SU R Cruickshank DPI: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.137 / SU Rfree Blow DPI: 0.117 / SU Rfree Cruickshank DPI: 0.114
Details: REFINEMENT NOTE 1, IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=NA CA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=11228. NUMBER WITH APPROX DEFAULT ...Details: REFINEMENT NOTE 1, IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=NA CA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=11228. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=4.
RfactorNum. reflection% reflectionSelection details
Rfree0.1979 6752 5.02 %RANDOM
Rwork0.1847 ---
obs0.1854 134445 97.31 %-
Displacement parametersBiso mean: 33.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.2306 Å20 Å20 Å2
2---0.6752 Å20 Å2
3---0.4447 Å2
Refine analyzeLuzzati coordinate error obs: 0.242 Å
Refinement stepCycle: LAST / Resolution: 1.98→28.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9707 0 242 1131 11080
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00710442HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9414347HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3258SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes187HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1572HARMONIC5
X-RAY DIFFRACTIONt_it10442HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.62
X-RAY DIFFRACTIONt_other_torsion14.29
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1355SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies25HARMONIC1
X-RAY DIFFRACTIONt_utility_distance2HARMONIC1
X-RAY DIFFRACTIONt_utility_angle4HARMONIC1
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact12290SEMIHARMONIC4
LS refinement shellResolution: 1.98→2.03 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2346 347 4.62 %
Rwork0.2206 7166 -
all0.2212 7513 -
obs--97.31 %
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)
11.9620.8649-0.40873.0287-0.49031.46430.0129-0.001-0.0343-0.01620.00520.11130.1029-0.1833-0.0181-0.0438-0.0377-0.0196-0.01590.0085-0.0535-40.5402-38.247328.5063
22.4684-0.132-0.16831.2345-0.13471.70540.0132-0.16550.05470.19540.00120.1613-0.0138-0.1043-0.0145-0.02560.01240.0657-0.0289-0.0113-0.0346-40.184-21.957943.5689
31.91640.8734-0.28181.9336-0.90592.34970.0212-0.172-0.18530.0135-0.0018-0.04750.0785-0.0084-0.0194-0.02620.02720.0037-0.03690.0358-0.0385-24.9805-38.206144.3322
40.60450.2269-0.5250.3074-0.48431.03060.01780.11630.0471-0.02750.00510.00170.0261-0.0671-0.0229-0.0320.01680.0073-0.0147-0.0048-0.0415-8.3255-10.9281-6.0225
50.41270.4602-0.31440.8041-0.4120.61770.0184-0.00940.05250.05630.00490.0367-0.13160.0143-0.0234-0.01050.0173-0.0123-0.04810.0028-0.0325-9.25138.855812.0076
60.76520.2544-0.49150.2195-0.16220.4832-0.0054-0.0164-0.0417-0.01510.0135-0.06420.02310.0427-0.0081-0.02780.0040.0023-0.0342-0.0144-0.01099.5219-9.957813.9236
72.773-0.4188-0.90430.9886-0.29021.3872-0.0117-0.06080.11790.08320.13480.2955-0.0061-0.2261-0.1231-0.09920.04420.030.02540.03760.0016-47.6969-10.776423.2608
80.802-0.1004-0.51932.2446-1.70833.23770.0294-0.1562-0.01260.23620.00250.0046-0.03650.11-0.03180.02840.004-0.0188-0.0259-0.011-0.088-12.682-18.376551.655
92.31322.21290.18333.5456-0.06680.90830.0095-0.0086-0.1706-0.0535-0.0407-0.03690.1523-0.11160.03120.0013-0.00790-0.0759-0.0359-0.0243-20.7266-47.388117.3055
101.84330.2053-0.97990.1002-1.91490.21820.00620.0202-0.00420.0580.0128-0.01220.0679-0.0132-0.019-0.0248-0.01020.0190.06560.0450.0418-55.8458-24.830134.9221
110.22591.1537-0.22540.2575-0.20590.72970.00310.0122-0.04050.0111-0.00890.0620.0008-0.02870.00580.06680.04-0.00360.04060.0018-0.0234-27.918-29.287259.7159
120.23780.2828-0.79770.8528-0.94470.1644-0.0031-0.0233-0.020.01350.0011-0.0108-0.002-0.0240.0020.0462-0.0032-0.0205-0.0084-0.00730.0534-32.4842-54.045932.3576
130.91820.46230.03990-0.14260.02840.0054-0.02290.0718-0.0156-0.0041-0.0184-0.0521-0.0789-0.0013-0.01890.01780.0353-0.02690.02910.024-23.00066.52138.5595
1400.37520.001900.53510.22320.01120.0294-0.0130.028-0.0099-0.08220.03940.1167-0.0013-0.03370.0121-0.00280.01690.04890.01636.6649-5.888827.5903
150.02350.1895-0.66710.6154-0.25960-0.00480.09920.00580.0002-0.00210.01760.0398-0.00360.0069-0.0131-0.0370.02340.0223-0.0182-0.0238-5.9614-24.6212-2.843
160.01510.0217-0.00380-0.0130.01420.00010.00360.0006-0.0061-0.00140.0024-0.0014-0.00130.00130.0099-0.0132-0.03870.02090.0109-0.0095-47.9083-31.602520.058
170.01780.0049-0.00590.0317-0.00770.0424-0.0001-0.00080.00070.00010.00060.00110.0013-0.0036-0.00060.01790.0133-0.00660.0386-0.0160.0432-16.709419.126710.1594
180.0021-0.0025-0.01260.0168-0.00260.02-0.00010.00160.00520.00020.0004-0.0017-0.00420.0004-0.00040.0218-0.00820.01680.0016-0.01830.0028-33.1564-13.845351.0674
190.01650.0009-0.03190.01330.014300.00050.0009-0.00020.0002-0.001-0.004400.00550.0005-0.00170.02260.01-0.0055-0.02010.0367-17.0924-46.386237.9064
200-0.00610.01880.00950.00370.003100.0026-0.0014-0.00090.00010.00070.0014-0.0002-0.00020.0110.0195-0.0103-0.0025-0.00530.013915.8912-24.32479.7509
210.0261-0.0005-0.02450.020.00190.0223-0.0006-0.0006-0.0044-0.0003-0.00030.0010.002-0.00070.00090.0380.0082-0.00870.0187-0.01440.0359-7.8759-19.2657-15.0956
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:30, 163:200, 318:327)
2X-RAY DIFFRACTION2(CHAIN B AND RESID 1:30, 163:200, 318:327)
3X-RAY DIFFRACTION3(CHAIN C AND RESID 1:30, 163:200, 318:327)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 31:162)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 31:162)
6X-RAY DIFFRACTION6(CHAIN C AND RESID 31:162)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 342:413)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 342:413)
9X-RAY DIFFRACTION9(CHAIN C AND RESID 342:413)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 328:341)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 328:341)
12X-RAY DIFFRACTION12(CHAIN C AND RESID 328:341)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 414:435)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 414:435)
15X-RAY DIFFRACTION15(CHAIN C AND RESID 414:435)
16X-RAY DIFFRACTION16(CHAIN A AND RESID 1436)
17X-RAY DIFFRACTION17(CHAIN A AND RESID 1437)
18X-RAY DIFFRACTION18(CHAIN B AND RESID 1436)
19X-RAY DIFFRACTION19(CHAIN C AND RESID 1436)
20X-RAY DIFFRACTION20(CHAIN C AND RESID 1437)
21X-RAY DIFFRACTION21(CHAIN C AND RESID 1438)

+
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