[English] 日本語
Yorodumi
- PDB-4k62: Structure of an avian influenza H5 hemagglutinin from the influen... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4k62
TitleStructure of an avian influenza H5 hemagglutinin from the influenza virus A/Indonesia/5/2005
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
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 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 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Aug 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 1.3Nov 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)220,86110
Polymers220,4198
Non-polymers4422
Water6,720373
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)165,9789
Polymers165,3146
Non-polymers6643
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area28700 Å2
ΔGint-132 kcal/mol
Surface area58770 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)165,9789
Polymers165,3146
Non-polymers6643
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_875-y+3,x-y+2,z1
crystal symmetry operation3_685-x+y+1,-x+3,z1
Buried area28480 Å2
ΔGint-139 kcal/mol
Surface area58330 Å2
MethodPISA
3
E: Hemagglutinin
F: Hemagglutinin

E: Hemagglutinin
F: Hemagglutinin

E: Hemagglutinin
F: Hemagglutinin


Theoretical massNumber of molelcules
Total (without water)165,3146
Polymers165,3146
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_865-y+3,x-y+1,z1
crystal symmetry operation3_785-x+y+2,-x+3,z1
Buried area28680 Å2
ΔGint-158 kcal/mol
Surface area57710 Å2
MethodPISA
4
G: Hemagglutinin
H: Hemagglutinin

G: Hemagglutinin
H: Hemagglutinin

G: Hemagglutinin
H: Hemagglutinin


Theoretical massNumber of molelcules
Total (without water)165,3146
Polymers165,3146
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_865-y+3,x-y+1,z1
crystal symmetry operation3_785-x+y+2,-x+3,z1
Buried area28160 Å2
ΔGint-156 kcal/mol
Surface area58400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.507, 70.507, 489.563
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-714-

HOH

21A-782-

HOH

31B-503-

HOH

41B-522-

HOH

51H-504-

HOH

-
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: 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.: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.41 %
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: 0.41
ReflectionResolution: 2.5→50 Å / Num. all: 85842 / Num. obs: 85842 / % possible obs: 90.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.5→2.59 Å / % possible all: 81.5

-
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

2fk0


Resolution: 2.502→48.887 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7749 / SU ML: 0.36 / σ(F): 1.96 / Phase error: 30.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2793 4284 4.99 %RANDOM
Rwork0.2355 ---
all0.2377 85804 --
obs0.2377 85804 91.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.86 Å2 / Biso mean: 34.2871 Å2 / Biso min: 0 Å2
Refinement stepCycle: LAST / Resolution: 2.502→48.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15476 0 28 373 15877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00615886
X-RAY DIFFRACTIONf_angle_d1.13721482
X-RAY DIFFRACTIONf_dihedral_angle_d16.8585848
X-RAY DIFFRACTIONf_chiral_restr0.0782288
X-RAY DIFFRACTIONf_plane_restr0.0052814
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.502-2.53040.36161050.3067233977
2.5304-2.56020.32851340.3001274594
2.5602-2.59140.37821440.2984287893
2.5914-2.62420.33511720.2827274894
2.6242-2.65870.36461410.289276394
2.6587-2.69510.32311260.2686284994
2.6951-2.73360.34011360.2705281594
2.7336-2.77440.3141440.2759279095
2.7744-2.81780.3441720.2819283593
2.8178-2.8640.33481520.2614272295
2.864-2.91340.31591580.2658283094
2.9134-2.96630.3141410.2564279794
2.9663-3.02340.28431470.2668274493
3.0234-3.08510.33781170.2562280293
3.0851-3.15210.31591500.2543273693
3.1521-3.22550.3121760.2498275091
3.2255-3.30610.28671370.2519272392
3.3061-3.39550.30871450.2438277291
3.3955-3.49540.24831360.2472268191
3.4954-3.60810.27541480.2186265891
3.6081-3.73710.26741470.222275390
3.7371-3.88660.28071300.216264989
3.8866-4.06340.24871260.2012269591
4.0634-4.27760.24711590.1985262990
4.2776-4.54540.21971560.2009265988
4.5454-4.8960.25221300.195263588
4.896-5.38820.26091500.2143263989
5.3882-6.16650.23421170.2216264389
6.1665-7.76420.24351470.2324268989
7.7642-48.89670.25371410.2313255286
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)
10.1228-0.0344-0.05990.0516-0.01340.1260.0136-0.25280.120.0583-0.0026-0.1164-0.0591-0.04370.00320.04560.0588-0.0065-0.1918-0.0695-0.054734.262484.787914.9571
2-0.013-0.0205-0.00820.0204-0.01530.01170.05480.051-0.0161-0.0192-0.06330.03030.011-0.0334-0.0306-0.6085-0.0853-0.0404-0.5608-0.0381-0.034239.70379.9276-26.2533
30.05880.00460.01180.0108-0.00030.00650.0277-0.117-0.00450.07050.0443-0.01710.0141-0.00230.05410.22290.0239-0.03190.09130.0143-0.014434.256882.664115.4393
40.00240.0012-0.00690.00090.00290.0049-0.0583-0.04110.02710.0013-0.0316-0.0275-0.0077-0.010600.2662-0.0359-0.01270.3247-0.06230.146634.386578.628454.3091
50.0076-0.00850.0080.0101-0.00970.00680.00640.04040.02210.0786-0.0153-0.006-0.04250.0135-00.2518-0.0325-0.02170.34390.02140.091243.677476.75741.2998
6-0.00150.00340.00110.0080.00120.0022-0.0212-0.01460.0123-0.00420.0151-0.01490.00840.00650.00010.1428-0.0001-0.0465-0.0122-0.03430.075335.426470.27821.3397
70.0328-0.00910.00610.03270.01970.0255-0.0377-0.1160.01880.05820.0178-0.019-0.00770.0197-0.02420.18660.09490.0370.1688-0.0901-0.141534.248367.862634.7063
80.00020.00120.00240.00140.00320.0055-0.01790.01380.00220.0070.0037-0.0177-0.01720.019-00.40260.0704-0.10560.4795-0.04430.159644.691776.243268.9632
90.0006-0.00120.00040.002900.0005-0.0066-0.0043-0.0255-0.04970.00560.00590.0030.00770.00230.2390.0420.07640.20490.05520.054739.555982.8986293.9492
100.00840.0263-0.00540.0717-0.00430.01170.048-0.0792-0.05230.1066-0.04080.03390.01860.0267-0.00050.02890.0536-0.0192-0.15930.01940.114935.742178.6046243.2657
110.0081-0.00830.01780.02330.00180.02050.0635-0.0006-0.0052-0.0326-0.05710.06590.0323-0.0072-0.0116-0.27760.01490.0012-0.1589-0.00580.176329.861182.6535216.4502
120.00470.0070.00680.00560.00210.00670.0135-0.0239-0.00140.07560.00440.0184-0.03940.01630.00520.2444-0.0011-0.00240.1405-0.00940.028436.23880.1511260.2138
130.0040.0010.00470.00590.00040.0027-0.033-0.043-0.03030.0432-0.0230.01230.05160.0183-00.2862-0.00410.02750.27550.04040.09836.083684.1661299.0821
140.0022-0.0013-0.00170.00960.00860.0057-0.0411-0.0159-0.01280.06490.00160.0130.01980.0058-00.3552-0.03330.05660.3319-0.00640.224926.859885.9898286.12
150.0437-0.02840.00570.0255-0.02740.0254-0.0442-0.0235-0.0037-0.00310.01560.00080.027-0.0105-0.02480.17060.0153-0.02620.05080.0306-0.034736.320794.8059267.1937
16-0.0001-0.00260.00240.0157-0.0240.028-0.0049-0.01360.01130.0314-0.0240.00240.0154-0.0135-0.01560.35770.08160.10720.40510.0728-0.051828.239588.1557313.2129
170.0051-0.0003-0.00310.00890.00980.00750.00210.0451-0.0122-0.02460.0057-0.00260.011-0.0069-0.0020.1622-0.1086-0.02220.2516-0.1210.157651.470476.8943171.9814
180.02120.02270.00490.0310.01240.00680.0162-0.16950.0540.0419-0.01830.0818-0.0335-0.0144-0.00410.2150.06330.05040.2375-0.02650.142645.973585.1813127.3191
19-0.00280.00070.0015-0.00140.0007-0.0012-0.0096-0.05330.0127-0.04320.02920.00260.0356-0.0236-00.17650.0517-0.01120.13180.02570.184952.479282.6404108.6717
200.11830.0236-0.07280.0486-0.01750.0642-0.03910.19530.1618-0.04440.02580.03070.0174-0.0989-0.00730.1835-0.0016-0.03830.15630.01310.187852.790190.007593.3084
21-0.00180.0061-0.00640.0052-0.00460.014-0.0466-0.09050.11250.1232-0.0370.0653-0.0256-0.03630.00020.2024-0.005-0.00090.2496-0.02290.127647.710789.5879115.9781
220.01370.00050.0032-0.00190.00040.001-0.0311-0.02220.0219-0.0117-0.00110.0442-0.02070.005300.459-0.17850.02720.605-0.05450.209453.375380.9401143.6397
230.00570.00330.00380.0072-0.00230.0083-0.00250.03390.00240.02130.0022-0.00360.02660.0081-00.22490.00530.04410.3903-0.01870.162851.457580.4461178.3797
240.0004-0.0003-0.00110.0046-0.00020.0005-0.0032-0.00940.0233-0.00180.004-0.0012-0.0237-0.017-00.3130.025-0.03020.32590.02730.200956.849590.921160.2452
250.0015-0.0028-0.00220.00310.00030.0013-0.0209-0.02290.01840.0119-0.0034-0.0014-0.0071-0.0124-00.2750.0466-0.05250.2773-0.08280.284460.965282.6942124.3815
26-0.0076-0.0105-0.00150.0145-0.00620.01410.0143-0.0643-0.03980.0147-0.04610.0043-0.01170.00380.00240.1887-0.00280.03950.2273-0.05230.106864.051179.9484151.9258
270.00420.0026-0.00670.0011-0.00440.00750.07480.02990.0852-0.02450.0725-0.0114-0.0383-0.0036-00.15160.04320.00220.1785-0.02830.205156.35586.9778191.7865
280.0060.0092-0.01260.0306-00.00910.02990.09810.08120.0015-0.01530.0291-0.0431-0.01070.00030.44890.00240.09940.32030.04450.035761.648762.5807-90.7788
290.0618-0.0024-0.00450.1823-0.05020.04020.04780.02440.0146-0.1813-0.04960.15260.0586-0.02270.010.15450.0223-0.01030.1519-0.02420.169854.108768.8633-145.7399
300.0030.0104-0.00270.00730.00560.0065-0.0269-0.0092-0.01560.05060.0040.0155-0.0351-0.032-00.62760.05830.04920.44420.01430.187859.11463.6199-106.4652
310.0079-0.00390.00760.0070.00040.0082-0.0414-0.03680.003-0.06380.00320.0175-0.01950.030500.3104-0.07620.02650.27370.03680.207861.889764.4565-66.3794
320.00260.0001-0.0002-0.0003-00.0001-0.016-0.01540.01850.01920.01140.02350.0037-0.0235-00.2934-0.0216-0.03440.3243-0.01550.229355.352274.0274-83.8337
330.0010.0013-0.00020.002-0.00090.00030.00060.00540.0006-0.02170.0022-0.00440.00210.0038-00.7892-0.03550.02730.8143-0.05070.787160.423775.5306-109.9523
340.0407-0.01830.0185-0.0038-0.01250.0332-0.0007-0.0155-0.01070.0689-0.0468-0.0858-0.0036-0.0311-0.00290.27630.02510.07170.20470.00880.143368.805274.7058-97.0348
350.0015-0.0011-0.00350.0037-0.00060.00440.0504-0.00780.0502-0.03970.07290.0350.0227-0.0529-00.22950.01480.0150.2249-0.00160.214758.640271.9327-52.92
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 4:85 )
2X-RAY DIFFRACTION2chain 'A' and (resseq 86:270 )
3X-RAY DIFFRACTION3chain 'A' and (resseq 271:324 )
4X-RAY DIFFRACTION4chain 'B' and (resseq 335:364 )
5X-RAY DIFFRACTION5chain 'B' and (resseq 365:393 )
6X-RAY DIFFRACTION6chain 'B' and (resseq 394:408 )
7X-RAY DIFFRACTION7chain 'B' and (resseq 409:471 )
8X-RAY DIFFRACTION8chain 'B' and (resseq 472:498 )
9X-RAY DIFFRACTION9chain 'C' and (resseq 4:23 )
10X-RAY DIFFRACTION10chain 'C' and (resseq 24:111 )
11X-RAY DIFFRACTION11chain 'C' and (resseq 112:270 )
12X-RAY DIFFRACTION12chain 'C' and (resseq 271:324 )
13X-RAY DIFFRACTION13chain 'D' and (resseq 335:364 )
14X-RAY DIFFRACTION14chain 'D' and (resseq 365:393 )
15X-RAY DIFFRACTION15chain 'D' and (resseq 394:460 )
16X-RAY DIFFRACTION16chain 'D' and (resseq 461:498 )
17X-RAY DIFFRACTION17chain 'E' and (resseq 4:23 )
18X-RAY DIFFRACTION18chain 'E' and (resseq 24:84 )
19X-RAY DIFFRACTION19chain 'E' and (resseq 85:111 )
20X-RAY DIFFRACTION20chain 'E' and (resseq 112:247 )
21X-RAY DIFFRACTION21chain 'E' and (resseq 248:289 )
22X-RAY DIFFRACTION22chain 'E' and (resseq 290:324 )
23X-RAY DIFFRACTION23chain 'F' and (resseq 335:371 )
24X-RAY DIFFRACTION24chain 'F' and (resseq 372:393 )
25X-RAY DIFFRACTION25chain 'F' and (resseq 394:408 )
26X-RAY DIFFRACTION26chain 'F' and (resseq 409:460 )
27X-RAY DIFFRACTION27chain 'F' and (resseq 461:498 )
28X-RAY DIFFRACTION28chain 'G' and (resseq 4:55 )
29X-RAY DIFFRACTION29chain 'G' and (resseq 56:270 )
30X-RAY DIFFRACTION30chain 'G' and (resseq 271:324 )
31X-RAY DIFFRACTION31chain 'H' and (resseq 335:371 )
32X-RAY DIFFRACTION32chain 'H' and (resseq 372:392 )
33X-RAY DIFFRACTION33chain 'H' and (resseq 393:402 )
34X-RAY DIFFRACTION34chain 'H' and (resseq 403:460 )
35X-RAY DIFFRACTION35chain 'H' and (resseq 461:498 )

+
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://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