[English] 日本語
Yorodumi
- PDB-4wa1: The crystal structure of hemagglutinin from a H3N8 influenza viru... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wa1
TitleThe crystal structure of hemagglutinin from a H3N8 influenza virus isolated from New England harbor seals
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN / hemagglutinin / influenza virus / seal
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.898 Å
AuthorsYang, H. / Villanueva, J.M. / Gubareva, L.V. / Stevens, J.
CitationJournal: J.Virol. / Year: 2015
Title: Structural and Functional Analysis of Surface Proteins from an A(H3N8) Influenza Virus Isolated from New England Harbor Seals.
Authors: Yang, H. / Nguyen, H.T. / Carney, P.J. / Guo, Z. / Chang, J.C. / Jones, J. / Davis, C.T. / Villanueva, J.M. / Gubareva, L.V. / Stevens, J.
History
DepositionAug 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Database references
Revision 2.0Nov 22, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / entity / entity_src_gen / pdbx_database_status / pdbx_struct_assembly_gen / pdbx_struct_oper_list / pdbx_validate_symm_contact / software / struct_conn / struct_site_gen
Item: _atom_site.label_asym_id / _atom_site.label_entity_id ..._atom_site.label_asym_id / _atom_site.label_entity_id / _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2 / _software.classification / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site_gen.label_asym_id
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / refine_hist / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Sep 27, 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 3.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
D: Hemagglutinin
E: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)340,31124
Polymers333,9736
Non-polymers6,33818
Water55,6663090
1
E: Hemagglutinin
F: Hemagglutinin
hetero molecules

A: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,15612
Polymers166,9873
Non-polymers3,1699
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area18150 Å2
ΔGint4 kcal/mol
Surface area57110 Å2
MethodPISA
2
B: Hemagglutinin
C: Hemagglutinin
D: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,15612
Polymers166,9873
Non-polymers3,1699
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18110 Å2
ΔGint2 kcal/mol
Surface area56940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.061, 103.155, 110.864
Angle α, β, γ (deg.)89.95, 90.00, 90.28
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Hemagglutinin


Mass: 55662.246 Da / Num. of mol.: 6 / Fragment: UNP residues 24-519
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/harbor seal/Massachusetts/1/2011(H3N8))
Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: I6NNE1
#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 8 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#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.: 8 / 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3090 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.65 %
Crystal growTemperature: 293 K / Method: microbatch / Details: 0.2 M ammonium iodide, 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 9, 2012
RadiationMonochromator: Rosenbaum-Rock double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.898→50 Å / Num. all: 280449 / Num. obs: 272212 / % possible obs: 97.1 % / Redundancy: 3.8 % / Net I/σ(I): 12.4

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2YP2

2yp2


Resolution: 1.898→46.779 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1949 13719 5.05 %
Rwork0.1696 --
obs0.1709 271660 96.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.898→46.779 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23160 0 414 3090 26664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00724102
X-RAY DIFFRACTIONf_angle_d1.13432632
X-RAY DIFFRACTIONf_dihedral_angle_d16.2018910
X-RAY DIFFRACTIONf_chiral_restr0.0793636
X-RAY DIFFRACTIONf_plane_restr0.0054240
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.898-1.91990.30384030.25447712X-RAY DIFFRACTION87
1.9199-1.94240.2544480.23388436X-RAY DIFFRACTION95
1.9424-1.96610.26444580.2148422X-RAY DIFFRACTION95
1.9661-1.9910.26184450.21158471X-RAY DIFFRACTION96
1.991-2.01720.24124600.2028542X-RAY DIFFRACTION96
2.0172-2.04490.2424180.19548488X-RAY DIFFRACTION96
2.0449-2.07410.2194590.18948481X-RAY DIFFRACTION96
2.0741-2.1050.21634770.18218551X-RAY DIFFRACTION96
2.105-2.13790.21624830.18058455X-RAY DIFFRACTION96
2.1379-2.1730.22764660.18448507X-RAY DIFFRACTION96
2.173-2.21040.22764310.17898540X-RAY DIFFRACTION96
2.2104-2.25060.21544620.18048547X-RAY DIFFRACTION96
2.2506-2.29390.24724980.18018567X-RAY DIFFRACTION97
2.2939-2.34070.21854450.17648585X-RAY DIFFRACTION97
2.3407-2.39160.21684310.16948589X-RAY DIFFRACTION97
2.3916-2.44730.21594610.17858742X-RAY DIFFRACTION97
2.4473-2.50850.19794490.17078659X-RAY DIFFRACTION98
2.5085-2.57630.2075040.17578653X-RAY DIFFRACTION98
2.5763-2.65210.20134710.17218659X-RAY DIFFRACTION98
2.6521-2.73770.18964580.16838686X-RAY DIFFRACTION98
2.7377-2.83550.20034600.17398763X-RAY DIFFRACTION98
2.8355-2.9490.18054880.16878702X-RAY DIFFRACTION98
2.949-3.08320.19564520.16878714X-RAY DIFFRACTION98
3.0832-3.24570.18554180.16398783X-RAY DIFFRACTION99
3.2457-3.4490.18364820.16118771X-RAY DIFFRACTION99
3.449-3.71520.17264550.15558743X-RAY DIFFRACTION99
3.7152-4.08890.16354650.14448803X-RAY DIFFRACTION99
4.0889-4.68010.14464630.13258773X-RAY DIFFRACTION99
4.6801-5.89460.16524610.1528810X-RAY DIFFRACTION99
5.8946-46.79340.18934480.18938787X-RAY DIFFRACTION99
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)
10.38430.0815-0.04110.4296-0.0599-0.1021-0.23810.15150.2371-0.33070.17070.3236-0.07110.0577-0.02630.2682-0.0444-0.03390.17820.04440.1132-58.8171-12.654433.5679
20.45260.0712-0.00660.6610.3140.6661-0.03980.0244-0.0318-0.01970.05860.0190.0141-0.01390.00220.15360.0232-0.00330.1412-0.00630.1093-77.6354-51.010836.3183
30.20570.21280.18110.14980.0598-0.0621-0.17130.14440.0809-0.17990.12560.0799-0.02460.071-0.00720.2356-0.04730.00060.18470.01410.1744-51.9297-7.638436.1748
40.0766-0.0022-0.01430.1442-0.00450.0868-0.16030.07440.042-0.17520.17490.08780.0067-0.05420.00050.2237-0.02360.00770.2122-0.00390.1608-50.5369-14.237539.6722
5-0.03770.11370.01190.384-0.03060.0087-0.090.10150.0372-0.0920.1059-0.0047-0.01150.01110.00010.1678-0.02180.00040.17450.00730.1547-31.51479.033244.7011
60.46480.0920.04740.26160.1283-0.0558-0.26420.2093-0.2644-0.34830.2161-0.32180.0602-0.0576-0.01280.2708-0.03780.03350.1511-0.0530.124-70.4863-2.9108-21.8795
70.34760.1259-0.03160.6887-0.40120.6075-0.04220.05380.0368-0.02780.0559-0.0002-0.01130.02930.00320.13780.01370.00020.116800.0871-51.658735.4375-19.1107
80.22690.1521-0.22760.0737-0.23590.1044-0.18770.1237-0.0778-0.22540.1695-0.05260.0734-0.07380.00070.2096-0.03220.00290.1324-0.01510.1464-70.4622.0464-18.8568
90.3214-0.03460.20290.0434-0.02180.1424-0.27670.3997-0.0042-0.17070.1593-0.08730.07830.16-0.05620.2547-0.08360.07930.2269-0.07160.2256-96.0338-34.8771-20.3237
100.01910.00780.07280.0345-0.04650.1269-0.20090.13350.0068-0.20850.2141-0.0267-0.0090.07520.00030.2271-0.03290.00270.1890.00380.1794-78.7846-1.3064-15.7318
110.01230.1322-0.01910.33210.01910.0291-0.09390.101-0.0141-0.07630.11120.01170.0166-0.0063-00.183-0.02970.00520.1539-0.00440.1653-97.7867-24.5785-10.7495
120.75020.71540.05980.5140.03320.36210.1742-0.3451-0.11360.1627-0.2181-0.14660.0952-0.0015-0.02230.231-0.0253-0.02650.20480.06640.2153-68.962-4.389716.8813
130.9395-0.2261-0.18660.3653-0.12750.45140.0672-0.0783-0.01550.0177-0.0434-0.1284-0.02840.08730.00010.13460.0136-0.0080.16640.00560.1457-40.259425.77527.1692
140.10340.16440.07690.10430.11020.19560.1492-0.1858-0.11480.1153-0.1535-0.09930.0871-0.004900.1904-0.0056-0.02020.17660.03990.2007-67.1861-0.874912.6078
150.27770.24610.1370.32570.15310.15310.1489-0.1693-0.06260.2123-0.1387-0.09380.0429-0.07140.10980.1816-0.0266-0.0190.15370.04620.1268-85.5496-15.50687.8047
160.0757-0.05890.01210.1177-0.0040.12660.2266-0.2958-0.25110.2087-0.1736-0.07440.1433-0.10480.00180.2695-0.0844-0.05390.22290.06650.259-106.2008-46.04166.4606
170.1845-0.020.0730.0933-0.02540.2053-0.0293-0.04490.0833-0.1058-0.03480.3966-0.0266-0.0740.00150.14480.0218-0.01870.195-0.00810.3446-102.28347.4743-3.9037
180.51010.0376-0.13190.4428-0.03830.78380.04230.01040.110.0217-0.0340.0488-0.05760.0994-00.14930.02320.01590.128-0.01060.1299-66.341144.61667.4556
19-0.03310.024-0.05650.3034-0.07930.0439-0.0128-0.03240.0497-0.0474-0.01270.1963-0.0266-0.01850.00550.11910.02670.00490.1253-0.03170.2001-89.779917.890.7625
20-0.01610.04770.05240.58750.05520.13540.04-0.03760.24210.036-0.04930.4032-0.0168-0.0316-0.22160.11450.01460.01670.1507-0.02250.2455-99.5887-3.5962-1.2358
210.176-0.01950.06630.0835-0.03410.10070.1305-0.07490.21880.1749-0.13770.5078-0.026-0.09970.00310.2476-0.05810.10760.266-0.02150.4657-123.9827-30.75622.5673
220.29890.3945-0.12240.3616-0.20770.17610.1532-0.23280.12680.1282-0.15180.1213-0.0768-0.02390.00250.1848-0.00520.04460.2103-0.05940.1831-72.3427-22.2686-40.2314
230.7754-0.22750.01790.21320.1810.42840.0494-0.0178-0.0051-0.0406-0.03180.1230.0453-0.15240.00270.13760.0311-0.0070.1852-0.00540.1609-89.4561-42.333-51.8485
240.01650.18320.0090.1199-0.21560.17730.2238-0.17470.0850.1807-0.21180.0961-0.08670.081100.227-0.03690.03470.2268-0.04630.2012-55.6135-11.0156-40.8557
250.14780.1429-0.19910.2848-0.21250.16070.1785-0.17550.09220.2265-0.16850.1414-0.05020.0740.01880.1812-0.020.02140.185-0.04140.1511-43.7522-0.1316-47.6084
260.0589-0.018-0.06430.1362-0.00510.13570.2731-0.33490.22180.3388-0.23450.0778-0.19370.16110.00180.3009-0.08660.06840.2586-0.05670.286-23.117430.4194-49.0146
270.0983-0.0654-0.02970.18110.1660.2033-0.0506-0.0458-0.1451-0.1985-0.0355-0.46170.04630.0877-0.00580.14760.02790.02130.24810.03690.3616-27.039-23.1307-59.3361
280.55070.08080.02710.5557-0.09770.66920.03720.0137-0.11580.0194-0.0459-0.04990.0611-0.0962-00.13070.0233-0.01370.14580.00780.1219-62.9588-60.2428-47.9716
29-0.0699-0.01250.00660.27030.06210.0645-0.0044-0.0112-0.056-0.0481-0.0259-0.19840.03190.0186-0.00030.12890.0237-0.00090.16850.03940.2196-39.5321-33.5277-54.6518
30-0.06240.0828-0.06950.6092-0.00360.12310.0524-0.0475-0.20820.0204-0.0684-0.36280.01350.0443-0.04190.10670.0163-0.010.17220.04190.2475-29.723-12.0547-56.6456
310.0935-0.00690.00340.0961-0.02680.04810.1138-0.1124-0.19850.1806-0.1727-0.5472-0.07230.1810.00030.2422-0.0779-0.08610.310.07320.4419-5.267615.0904-52.8555
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 89 )
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 249 )
3X-RAY DIFFRACTION3chain 'A' and (resid 250 through 366 )
4X-RAY DIFFRACTION4chain 'A' and (resid 367 through 404 )
5X-RAY DIFFRACTION5chain 'A' and (resid 405 through 503 )
6X-RAY DIFFRACTION6chain 'B' and (resid 8 through 89 )
7X-RAY DIFFRACTION7chain 'B' and (resid 90 through 249 )
8X-RAY DIFFRACTION8chain 'B' and (resid 250 through 337 )
9X-RAY DIFFRACTION9chain 'B' and (resid 338 through 366 )
10X-RAY DIFFRACTION10chain 'B' and (resid 367 through 404 )
11X-RAY DIFFRACTION11chain 'B' and (resid 405 through 503 )
12X-RAY DIFFRACTION12chain 'C' and (resid 8 through 89 )
13X-RAY DIFFRACTION13chain 'C' and (resid 90 through 249 )
14X-RAY DIFFRACTION14chain 'C' and (resid 250 through 337 )
15X-RAY DIFFRACTION15chain 'C' and (resid 338 through 461 )
16X-RAY DIFFRACTION16chain 'C' and (resid 462 through 503 )
17X-RAY DIFFRACTION17chain 'D' and (resid 8 through 65 )
18X-RAY DIFFRACTION18chain 'D' and (resid 66 through 249 )
19X-RAY DIFFRACTION19chain 'D' and (resid 250 through 337 )
20X-RAY DIFFRACTION20chain 'D' and (resid 338 through 461 )
21X-RAY DIFFRACTION21chain 'D' and (resid 462 through 503 )
22X-RAY DIFFRACTION22chain 'E' and (resid 8 through 153 )
23X-RAY DIFFRACTION23chain 'E' and (resid 154 through 265 )
24X-RAY DIFFRACTION24chain 'E' and (resid 266 through 337 )
25X-RAY DIFFRACTION25chain 'E' and (resid 338 through 461 )
26X-RAY DIFFRACTION26chain 'E' and (resid 462 through 503 )
27X-RAY DIFFRACTION27chain 'F' and (resid 8 through 65 )
28X-RAY DIFFRACTION28chain 'F' and (resid 66 through 249 )
29X-RAY DIFFRACTION29chain 'F' and (resid 250 through 337 )
30X-RAY DIFFRACTION30chain 'F' and (resid 338 through 461 )
31X-RAY DIFFRACTION31chain 'F' and (resid 462 through 503 )

+
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