[English] 日本語
Yorodumi
- PDB-4k63: Structure of an avian influenza H5 hemagglutinin from the influen... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4k63
TitleStructure of an avian influenza H5 hemagglutinin from the influenza virus complexed with avian receptor analog LSTa
Components(Hemagglutinin) x 2
KeywordsVIRAL PROTEIN / virus attachment / membrane fusion
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / 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
Similarity search - Function
Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / 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 ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / 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 / Ribbon / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
3'-sialyl-N-acetyllactosamine / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsZhang, W. / Shi, Y. / Lu, X. / Shu, Y. / Qi, J. / Gao, G.F.
CitationJournal: Science / Year: 2013
Title: An airborne transmissible avian influenza H5 hemagglutinin seen at the atomic level.
Authors: Zhang, W. / Shi, Y. / Lu, X. / Shu, Y. / Qi, J. / Gao, G.F.
History
DepositionApr 15, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 24, 2022Group: Database references / Structure summary / Category: chem_comp / citation / database_2
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)223,35714
Polymers220,4198
Non-polymers2,9386
Water00
1
A: Hemagglutinin
B: Hemagglutinin
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,00212
Polymers165,3146
Non-polymers2,6876
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-y,x-y+2,z1
crystal symmetry operation3_355-x+y-2,-x,z1
Buried area31060 Å2
ΔGint-123 kcal/mol
Surface area59830 Å2
MethodPISA
2
C: Hemagglutinin
D: Hemagglutinin
hetero molecules

C: Hemagglutinin
D: Hemagglutinin
hetero molecules

C: Hemagglutinin
D: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,3389
Polymers165,3146
Non-polymers2,0243
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_685-y+1,x-y+3,z1
crystal symmetry operation3_365-x+y-2,-x+1,z1
Buried area30240 Å2
ΔGint-140 kcal/mol
Surface area59680 Å2
MethodPISA
3
E: Hemagglutinin
F: Hemagglutinin
hetero molecules

E: Hemagglutinin
F: Hemagglutinin
hetero molecules

E: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,39212
Polymers165,3146
Non-polymers2,0786
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_585-y,x-y+3,z1
crystal symmetry operation3_255-x+y-3,-x,z1
Buried area30230 Å2
ΔGint-126 kcal/mol
Surface area59320 Å2
MethodPISA
4
G: Hemagglutinin
H: Hemagglutinin
hetero molecules

G: Hemagglutinin
H: Hemagglutinin
hetero molecules

G: Hemagglutinin
H: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,3389
Polymers165,3146
Non-polymers2,0243
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_685-y+1,x-y+3,z1
crystal symmetry operation3_365-x+y-2,-x+1,z1
Buried area30230 Å2
ΔGint-140 kcal/mol
Surface area59770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.555, 70.555, 506.295
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

-
Components

#1: Protein
Hemagglutinin


Mass: 36193.895 Da / Num. of mol.: 4 / Fragment: UNP residues 17-326
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Indonesia/5/2005(H5N1) / Gene: HA / Plasmid: pFastBac1 / Cell line (production host): Hi5 / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: A8HWY8
#2: Protein
Hemagglutinin


Mass: 18910.838 Da / Num. of mol.: 4 / Fragment: UNP residues 347-510
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Indonesia/5/2005(H5N1) / Gene: HA / Plasmid: pFastBac1 / Cell line (production host): Hi5 / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: A8HWY8
#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 3'-sialyl-N-acetyllactosamine


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 674.604 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 3'-sialyl-N-acetyllactosamine
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#4: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a3-b2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
#5: 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.: 2
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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG 2000 MME, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 3, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinType: merohedral / Operator: -h,-k,l / Fraction: 0.428
ReflectionResolution: 3.1→50 Å / Num. all: 42807 / Num. obs: 42807 / % possible obs: 82 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 57.19 Å2
Reflection shellResolution: 3.1→3.21 Å / % possible all: 83.3

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FK0
Resolution: 3.1→49.49 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7261 / SU ML: 0.43 / σ(F): 1.99 / Phase error: 34.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3069 2162 5.05 %RANDOM
Rwork0.245 ---
all0.2481 42793 --
obs0.2481 42793 80.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 202.92 Å2 / Biso mean: 67.4869 Å2 / Biso min: 0 Å2
Refinement stepCycle: LAST / Resolution: 3.1→49.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15476 0 198 0 15674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416063
X-RAY DIFFRACTIONf_angle_d1.08221744
X-RAY DIFFRACTIONf_dihedral_angle_d17.5465917
X-RAY DIFFRACTIONf_chiral_restr0.1262351
X-RAY DIFFRACTIONf_plane_restr0.0042825
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0646-3.13590.39351080.3115219367
3.1359-3.21430.38071390.2812285882
3.2143-3.30120.3511510.2808275585
3.3012-3.39830.29451460.2724279883
3.3983-3.50790.39071660.2901277483
3.5079-3.63330.32911650.268269482
3.6333-3.77870.32371580.2677271582
3.7787-3.95060.30891530.2543276181
3.9506-4.15880.27881260.2548270980
4.1588-4.41920.31631510.2343267280
4.4192-4.76020.34761470.2274266881
4.7602-5.23870.27021140.224271080
5.2387-5.99570.31121460.2295268180
5.9957-7.54960.25481420.2325269580
7.5496-49.49650.24151500.2064294886
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.02840.00440.08620.0065-0.01560.1306-0.06820.09940.062-0.1052-0.00230.0494-0.1541-0.0106-0.53320.06580.0093-0.1138-0.05770.0484-0.3254-89.272552.9383-7.4064
20.1939-0.05990.110.2244-0.01790.8162-0.1725-0.05610.09850.1227-0.09560.0946-0.0544-0.1331-1.8805-0.03610.032-0.07070.00280.024-0.179-89.897345.506728.6169
30.0009-0.0113-0.00250.0260.00410.0010.07210.086-0.0185-0.0026-0.1166-0.02470.1017-0.1412-0.03390.52690.1527-0.00290.49190.02770.1918-88.69852.5384-15.0348
4-0.001-0.0149-0.00270.07020.02620.0092-0.04710.15030.0801-0.0976-0.09440.03270.01970.001-0.0260.8283-0.0489-0.12850.84830.05410.2655-87.078546.3682-47.8083
50.3949-0.0188-0.080.19330.01630.11330.00910.206-0.007-0.1294-0.02280.0595-0.0341-0.0458-0.02810.1665-0.0071-0.1086-0.00960.0853-0.1382-75.865945.574-19.7364
60.02550.0386-0.00640.06390.00090.01560.04430.0445-0.00790.0720.10450.125-0.0076-0.0529-0.00011.1949-0.0246-0.17711.21490.06480.3522-85.975341.8576-67.3288
70.0333-0.01760.03110.02440.03160.04-0.06510.2046-0.094-0.0538-0.09250.019-0.0809-0.1013-0.43480.139-0.0135-0.13620.3228-0.11830.0346-90.498471.5051-134.8426
80.3367-0.1216-0.04780.1563-0.04930.05980.0606-0.14580.0243-0.02740.0120.0018-0.12670.04920.1775-0.02750.09450.12370.0157-0.0960.0124-84.380467.162-98.8229
90.06270.03230.03660.02240.03030.0375-0.0287-0.01410.0058-0.02440.03250.03370.0348-0.04630.0090.4192-0.0502-0.11370.5814-0.06670.132-89.941971.8763-142.4038
100.0977-0.0280.00430.0058-0.00630.032-0.11730.0103-0.0375-0.08830.020.0750.0822-0.08630.00450.9814-0.0926-0.05051.1832-0.11890.301-83.766470.3344-175.3012
110.0065-0.0192-0.00630.1134-0.01280.0157-0.05570.0876-0.0022-0.2121-0.03050.0324-0.0132-0.0736-0.19970.339-0.0928-0.1110.2371-0.05950.1256-77.441779.3926-147.2038
120.00010.0004-0.0004-0.0003-0-0.00010.0278-0.0386-0.03340.02090.0786-0.02360.066-0.108501.2820.1574-0.05571.482-0.12960.7606-79.106268.7381-194.8448
130.07110.09680.04580.1060.05050.02530.0572-0.0414-0.0360.055-0.0687-0.1540.1730.0550.00060.16140.07030.00030.2078-0.03780.315-87.128348.8915-260.4965
140.135-0.0504-0.10290.15460.03240.0893-0.0934-0.17370.06390.10680.0248-0.1537-0.00120.0983-0.04640.10650.0386-0.03150.19610.00970.4917-86.4856.2985-224.4271
150.0206-0.022-0.01330.01560.01380.0104-0.08490.1564-0.0901-0.1076-0.10140.13160.10150.0075-00.456-0.00930.09870.3872-0.01330.6496-87.638649.229-268.1503
160.0007-0.0033-0.00280.0090.00440.002-0.0294-0.00860.0506-0.115-0.01760.09180.0724-0.0086-01.11020.12990.28050.8263-0.13670.8541-91.147751.1222-306.6216
170.0087-0.00390.00840.0043-0.00290.0065-0.00090.0110.05970.1085-0.07410.0377-0.0110.024800.7794-0.21940.0820.7527-0.0450.7923-87.783260.293-293.8137
180.02270.02470.01170.0332-0.00180.0916-0.118-0.00730.0607-0.04010.0687-0.0324-0.04250.0076-0.01130.36550.07430.11180.4004-0.09630.528-97.666256.5426-254.1413
190.13810.0461-0.03530.022-0.0010.04240.1136-0.00960.0704-0.1616-0.0660.0181-0.0538-0.00630.04590.62590.15410.01180.2736-0.02720.1889-101.139556.5358-280.3567
200.00450.00110.00360.001-0.00060.00290.04580.0513-0.00310.03560.0769-0.091-0.0085-0.0096-01.31-0.28810.12811.1503-0.01090.5701-90.042659.8117-320.7185
210.2114-0.09140.01170.0378-0.00310.0358-0.12210.0885-0.3227-0.03260.02170.02040.0218-0.1148-0.0870.3735-0.0519-0.03140.2046-0.06670.5259-71.964859.1826118.2642
220.2083-0.00020.19540.37920.06830.27140.0361-0.0757-0.040.1803-0.039-0.1014-0.0462-0.0465-0.06180.14790.01760.01020.14960.07060.4636-65.033662.3389154.2371
230.0228-0.0287-0.01110.02780.00810.0142-0.00580.07860.0182-0.063-0.03030.21190.01620.042900.71830.01470.12710.7139-0.06730.6228-71.882260.0069110.6384
240.01370.0197-0.00790.022-0.00550.00590.0512-0.0287-0.0282-0.06580.05340.01070.06740.009201.1837-0.31390.02521.0811-0.14890.8831-67.467164.269177.883
250.08290.04540.02160.0866-0.00160.0180.01880.098-0.2074-0.1464-0.06840.10090.0305-0.04490.00880.4232-0.08740.0120.3943-0.07740.2951-72.181374.4155105.7946
26-0.00010.001900.00860.00150.00250.0779-0.0682-0.04340.0481-0.01920.00890.07110.0198-01.381-0.1699-0.03731.4019-0.03260.8359-63.705367.453858.3236
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 4:111 )A4 - 111
2X-RAY DIFFRACTION2chain 'A' and (resseq 112:270 )A112 - 270
3X-RAY DIFFRACTION3chain 'A' and (resseq 271:324 )A271 - 324
4X-RAY DIFFRACTION4chain 'B' and (resseq 335:393 )B335 - 393
5X-RAY DIFFRACTION5chain 'B' and (resseq 394:457 )B394 - 457
6X-RAY DIFFRACTION6chain 'B' and (resseq 458:498 )B458 - 498
7X-RAY DIFFRACTION7chain 'C' and (resseq 4:111 )C4 - 111
8X-RAY DIFFRACTION8chain 'C' and (resseq 112:270 )C112 - 270
9X-RAY DIFFRACTION9chain 'C' and (resseq 271:324 )C271 - 324
10X-RAY DIFFRACTION10chain 'D' and (resseq 335:393 )D335 - 393
11X-RAY DIFFRACTION11chain 'D' and (resseq 394:457 )D394 - 457
12X-RAY DIFFRACTION12chain 'D' and (resseq 458:498 )D458 - 498
13X-RAY DIFFRACTION13chain 'E' and (resseq 4:111 )E4 - 111
14X-RAY DIFFRACTION14chain 'E' and (resseq 112:270 )E112 - 270
15X-RAY DIFFRACTION15chain 'E' and (resseq 271:324 )E271 - 324
16X-RAY DIFFRACTION16chain 'F' and (resseq 335:364 )F335 - 364
17X-RAY DIFFRACTION17chain 'F' and (resseq 365:393 )F365 - 393
18X-RAY DIFFRACTION18chain 'F' and (resseq 394:408 )F394 - 408
19X-RAY DIFFRACTION19chain 'F' and (resseq 409:459 )F409 - 459
20X-RAY DIFFRACTION20chain 'F' and (resseq 460:498 )F460 - 498
21X-RAY DIFFRACTION21chain 'G' and (resseq 4:111 )G4 - 111
22X-RAY DIFFRACTION22chain 'G' and (resseq 112:270 )G112 - 270
23X-RAY DIFFRACTION23chain 'G' and (resseq 271:324 )G271 - 324
24X-RAY DIFFRACTION24chain 'H' and (resseq 335:393 )H335 - 393
25X-RAY DIFFRACTION25chain 'H' and (resseq 394:457 )H394 - 457
26X-RAY DIFFRACTION26chain 'H' and (resseq 458:498 )H458 - 498

+
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://pdbjlvh1.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