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- PDB-6d7c: The crystal structure of hemagglutinin from A/Hong Kong/61/2016 H... -

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Basic information

Entry
Database: PDB / ID: 6d7c
TitleThe crystal structure of hemagglutinin from A/Hong Kong/61/2016 H7N9 influenza virus
Components
  • Hemagglutinin HA1 chain
  • Hemagglutinin HA2 chain
KeywordsVIRAL PROTEIN / Influenza virus / Surface protein / H7N9
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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 / virion 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
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsYang, H. / Stevens, J.
CitationJournal: J. Virol. / Year: 2018
Title: Structural and Molecular Characterization of the Hemagglutinin from the Fifth-Epidemic-Wave A(H7N9) Influenza Viruses.
Authors: Yang, H. / Carney, P.J. / Chang, J.C. / Guo, Z. / Stevens, J.
History
DepositionApr 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 3, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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 / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 4, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
C: Hemagglutinin HA1 chain
D: Hemagglutinin HA2 chain
E: Hemagglutinin HA1 chain
F: Hemagglutinin HA2 chain
G: Hemagglutinin HA1 chain
H: Hemagglutinin HA2 chain
I: Hemagglutinin HA1 chain
J: Hemagglutinin HA2 chain
K: Hemagglutinin HA1 chain
L: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)363,80922
Polymers361,59612
Non-polymers2,21210
Water0
1
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
E: Hemagglutinin HA1 chain
F: Hemagglutinin HA2 chain
I: Hemagglutinin HA1 chain
J: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,12512
Polymers180,7986
Non-polymers1,3276
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34200 Å2
ΔGint-146 kcal/mol
Surface area55650 Å2
MethodPISA
2
C: Hemagglutinin HA1 chain
D: Hemagglutinin HA2 chain
G: Hemagglutinin HA1 chain
H: Hemagglutinin HA2 chain
K: Hemagglutinin HA1 chain
L: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,68310
Polymers180,7986
Non-polymers8854
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33940 Å2
ΔGint-156 kcal/mol
Surface area55170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.014, 97.527, 191.809
Angle α, β, γ (deg.)90.00, 108.58, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13A
23G
14A
24I
15A
25K
16B
26D
17B
27F
18B
28H
19B
29J
110B
210L
111C
211E
112C
212G
113C
213I
114C
214K
115D
215F
116D
216H
117D
217J
118D
218L
119E
219G
120E
220I
121E
221K
122F
222H
123F
223J
124F
224L
125G
225I
126G
226K
127H
227J
128H
228L
129I
229K
130J
230L

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPGLUGLUAA1 - 3161 - 316
21ASPASPGLUGLUCC1 - 3161 - 316
12ASPASPGLUGLUAA1 - 3161 - 316
22ASPASPGLUGLUEE1 - 3161 - 316
13ASPASPGLUGLUAA1 - 3161 - 316
23ASPASPGLUGLUGG1 - 3161 - 316
14ASPASPGLUGLUAA1 - 3161 - 316
24ASPASPGLUGLUII1 - 3161 - 316
15ASPASPGLUGLUAA1 - 3161 - 316
25ASPASPGLUGLUKK1 - 3161 - 316
16GLYGLYILEILEBB1 - 1711 - 171
26GLYGLYILEILEDD1 - 1711 - 171
17GLYGLYILEILEBB1 - 1711 - 171
27GLYGLYILEILEFF1 - 1711 - 171
18GLYGLYILEILEBB1 - 1711 - 171
28GLYGLYILEILEHH1 - 1711 - 171
19GLYGLYILEILEBB1 - 1711 - 171
29GLYGLYILEILEJJ1 - 1711 - 171
110GLYGLYILEILEBB1 - 1711 - 171
210GLYGLYILEILELL1 - 1711 - 171
111ASPASPGLUGLUCC1 - 3161 - 316
211ASPASPGLUGLUEE1 - 3161 - 316
112ASPASPGLUGLUCC1 - 3161 - 316
212ASPASPGLUGLUGG1 - 3161 - 316
113ASPASPGLUGLUCC1 - 3161 - 316
213ASPASPGLUGLUII1 - 3161 - 316
114ASPASPGLUGLUCC1 - 3161 - 316
214ASPASPGLUGLUKK1 - 3161 - 316
115GLYGLYILEILEDD1 - 1711 - 171
215GLYGLYILEILEFF1 - 1711 - 171
116GLYGLYILEILEDD1 - 1711 - 171
216GLYGLYILEILEHH1 - 1711 - 171
117GLYGLYILEILEDD1 - 1711 - 171
217GLYGLYILEILEJJ1 - 1711 - 171
118GLYGLYILEILEDD1 - 1711 - 171
218GLYGLYILEILELL1 - 1711 - 171
119ASPASPGLUGLUEE1 - 3161 - 316
219ASPASPGLUGLUGG1 - 3161 - 316
120ASPASPGLUGLUEE1 - 3161 - 316
220ASPASPGLUGLUII1 - 3161 - 316
121ASPASPGLUGLUEE1 - 3161 - 316
221ASPASPGLUGLUKK1 - 3161 - 316
122GLYGLYILEILEFF1 - 1711 - 171
222GLYGLYILEILEHH1 - 1711 - 171
123GLYGLYILEILEFF1 - 1711 - 171
223GLYGLYILEILEJJ1 - 1711 - 171
124GLYGLYILEILEFF1 - 1711 - 171
224GLYGLYILEILELL1 - 1711 - 171
125ASPASPGLUGLUGG1 - 3161 - 316
225ASPASPGLUGLUII1 - 3161 - 316
126ASPASPGLUGLUGG1 - 3161 - 316
226ASPASPGLUGLUKK1 - 3161 - 316
127GLYGLYILEILEHH1 - 1711 - 171
227GLYGLYILEILEJJ1 - 1711 - 171
128GLYGLYILEILEHH1 - 1711 - 171
228GLYGLYILEILELL1 - 1711 - 171
129ASPASPGLUGLUII1 - 3161 - 316
229ASPASPGLUGLUKK1 - 3161 - 316
130GLYGLYILEILEJJ1 - 1711 - 171
230GLYGLYILEILELL1 - 1711 - 171

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30

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Components

#1: Protein
Hemagglutinin HA1 chain


Mass: 34991.652 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Hong Kong/61/2016(H7N9) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0C4ZYE2
#2: Protein
Hemagglutinin HA2 chain


Mass: 25274.420 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Hong Kong/61/2016(H7N9) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: S4V1Z7
#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.: 10
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

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.23 %
Crystal growTemperature: 293 K / Method: microbatch
Details: 0.2 M Magnesium Chloride, 0.1M HEPES:NaOH, pH7.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 68692 / % possible obs: 93.1 % / Redundancy: 3.1 % / Net I/σ(I): 6.43
Reflection shellResolution: 2.95→3.06 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LN6
Resolution: 2.95→50 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.877 / SU B: 51.077 / SU ML: 0.401 / Cross valid method: THROUGHOUT / ESU R Free: 0.474 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26703 3659 5.1 %RANDOM
Rwork0.2363 ---
obs0.23783 68692 93.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 66.234 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å20.98 Å2
2---4.06 Å20 Å2
3---2.27 Å2
Refinement stepCycle: 1 / Resolution: 2.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22800 0 140 0 22940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01923394
X-RAY DIFFRACTIONr_bond_other_d0.0020.0221003
X-RAY DIFFRACTIONr_angle_refined_deg1.8961.94431612
X-RAY DIFFRACTIONr_angle_other_deg1.067348835
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.59852910
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.64824.4561158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.011154008
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.85615168
X-RAY DIFFRACTIONr_chiral_restr0.1020.23418
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0226422
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024823
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5144.14911676
X-RAY DIFFRACTIONr_mcbond_other2.5144.1511675
X-RAY DIFFRACTIONr_mcangle_it4.1516.22414574
X-RAY DIFFRACTIONr_mcangle_other4.1516.22414575
X-RAY DIFFRACTIONr_scbond_it2.4984.34411718
X-RAY DIFFRACTIONr_scbond_other2.4984.34511719
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1426.43317039
X-RAY DIFFRACTIONr_long_range_B_refined6.25347.34325276
X-RAY DIFFRACTIONr_long_range_B_other6.25347.34525277
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A198920.02
12C198920.02
21A198480.02
22E198480.02
31A198900.01
32G198900.01
41A197820.02
42I197820.02
51A197860.02
52K197860.02
61B109360.01
62D109360.01
71B109340.01
72F109340.01
81B109440.01
82H109440.01
91B109320.01
92J109320.01
101B109580.01
102L109580.01
111C198740.02
112E198740.02
121C198760.01
122G198760.01
131C198460.02
132I198460.02
141C198260.02
142K198260.02
151D109260.01
152F109260.01
161D109320.01
162H109320.01
171D109240.01
172J109240.01
181D109240.01
182L109240.01
191E198580.01
192G198580.01
201E198220.02
202I198220.02
211E198380.01
212K198380.01
221F109420.01
222H109420.01
231F109220.01
232J109220.01
241F109380.01
242L109380.01
251G198240.02
252I198240.02
261G198220.01
262K198220.01
271H109280.01
272J109280.01
281H109540.01
282L109540.01
291I198480.02
292K198480.02
301J109260.01
302L109260.01
LS refinement shellResolution: 2.95→3.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 206 -
Rwork0.318 3724 -
obs--69.55 %
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)
10.0077-0.0391-0.06350.45980.48471.10810.01750.0148-0.00130.09520.0008-0.03260.129-0.0151-0.01820.290.00250.01750.370.01660.0821-30.3824-29.7369-7.0109
20.13340.12310.40830.49540.36041.50510.13910.0534-0.01990.2704-0.1274-0.16050.3489-0.0526-0.01170.5769-0.1319-0.06590.38940.01170.0639-31.3773-21.088442.4924
30.10270.1434-0.22640.2665-0.15331.03-0.01260.018-0.09540.0613-0.0896-0.1620.1459-0.22340.10220.2778-0.0652-0.00340.38220.00480.1114-11.0262-71.086392.7206
40.02760.0096-0.2110.05060.02981.8941-0.01190.00390.0183-0.00470.04310.04460.0573-0.0741-0.03120.2973-0.02760.00770.4222-0.04170.0592-5.7525-65.52742.5346
50.0920.0522-0.25420.16250.09481.20270.043-0.0258-0.0097-0.0117-0.0226-0.0632-0.13920.0004-0.02040.3285-0.03280.03530.34150.00710.0787-20.60261.0997-8.0287
60.11810.12470.1560.22660.23151.45730.1478-0.01960.03880.0383-0.06480.0623-0.0363-0.1505-0.0830.4025-0.10760.06330.4131-0.06330.0452-30.2212-0.470741.7586
70.3599-0.4273-0.36730.66750.16162.0877-0.179-0.0173-0.26690.19960.09420.3438-0.3990.07080.08480.40390.02470.19090.30150.00990.217-0.6557-40.581492.162
80.11760.0119-0.33970.1596-0.1011.07820.0822-0.02230.035-0.0317-0.0171-0.0365-0.1871-0.068-0.0650.3180.01680.03180.36480.00480.08315.4946-47.924442.9318
90.3315-0.0561-0.36160.2763-0.02520.9950.21970.05250.1259-0.0791-0.2683-0.0752-0.0061-0.12140.04860.38870.08010.08080.3570.01240.1391-51.9913-6.3587-9.1876
100.09330.1023-0.03740.29790.20191.88020.1263-0.02640.0470.1332-0.23660.09730.3155-0.29060.11030.39-0.21330.09640.4718-0.08980.0404-48.8547-9.722441.117
110.17450.1510.31620.1980.50883.19550.0124-0.07390.0104-0.0059-0.1111-0.02080.20930.22830.09870.25590.0234-0.03720.35010.00830.108320.224-64.964894.2421
120.1305-0.0951-0.51960.14750.57092.5588-0.0423-0.0428-0.0460.02290.0141-0.03030.12820.05550.02820.3090.01350.07630.3539-0.00570.09515.0184-66.398543.8617
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 316
2X-RAY DIFFRACTION2B1 - 171
3X-RAY DIFFRACTION3C1 - 316
4X-RAY DIFFRACTION4D1 - 171
5X-RAY DIFFRACTION5E1 - 316
6X-RAY DIFFRACTION6F1 - 171
7X-RAY DIFFRACTION7G1 - 316
8X-RAY DIFFRACTION8H1 - 171
9X-RAY DIFFRACTION9I1 - 316
10X-RAY DIFFRACTION10J1 - 171
11X-RAY DIFFRACTION11K1 - 316
12X-RAY DIFFRACTION12L1 - 171

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  • 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

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