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- PDB-4wst: The crystal structure of hemagglutinin from A/Taiwan/1/2013 influ... -

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Basic information

Entry
Database: PDB / ID: 4wst
TitleThe crystal structure of hemagglutinin from A/Taiwan/1/2013 influenza virus
Components
  • Hemagglutinin HA1 chain
  • Hemagglutinin HA2 chain
KeywordsVIRAL PROTEIN / Hemagglutinin / influenza virus / H6
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
Haemagglutinin, influenzavirus 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 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 HA2 chain / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsYang, H. / Carney, P.J. / Chang, J. / Villanueva, J.M. / Stevens, J.
CitationJournal: J.Virol. / Year: 2015
Title: Structure and receptor binding preferences of recombinant hemagglutinins from avian and human h6 and h10 influenza a virus subtypes.
Authors: Yang, H. / Carney, P.J. / Chang, J.C. / Villanueva, J.M. / Stevens, J.
History
DepositionOct 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp / citation ...chem_comp / citation / database_PDB_caveat / entity / entity_src_gen / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 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 / 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)352,90130
Polymers348,91912
Non-polymers3,98218
Water13,403744
1
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
G: Hemagglutinin HA1 chain
H: Hemagglutinin HA2 chain
I: Hemagglutinin HA1 chain
J: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,45115
Polymers174,4606
Non-polymers1,9919
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30650 Å2
ΔGint-140 kcal/mol
Surface area59890 Å2
MethodPISA
2
C: Hemagglutinin HA1 chain
D: Hemagglutinin HA2 chain
E: Hemagglutinin HA1 chain
F: Hemagglutinin HA2 chain
K: Hemagglutinin HA1 chain
L: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,45115
Polymers174,4606
Non-polymers1,9919
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30700 Å2
ΔGint-141 kcal/mol
Surface area59770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)226.630, 100.612, 175.477
Angle α, β, γ (deg.)90.00, 99.66, 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
11SERSERPROPROAA0 - 3245 - 329
21SERSERPROPROCC0 - 3245 - 329
12SERSERPROPROAA0 - 3245 - 329
22SERSERPROPROEE0 - 3245 - 329
13SERSERPROPROAA0 - 3245 - 329
23SERSERPROPROGG0 - 3245 - 329
14SERSERPROPROAA0 - 3245 - 329
24SERSERPROPROII0 - 3245 - 329
15SERSERPROPROAA0 - 3245 - 329
25SERSERPROPROKK0 - 3245 - 329
16GLYGLYLEULEUBB1 - 1681 - 168
26GLYGLYLEULEUDD1 - 1681 - 168
17GLYGLYLEULEUBB1 - 1681 - 168
27GLYGLYLEULEUFF1 - 1681 - 168
18GLYGLYLEULEUBB1 - 1681 - 168
28GLYGLYLEULEUHH1 - 1681 - 168
19GLYGLYLEULEUBB1 - 1681 - 168
29GLYGLYLEULEUJJ1 - 1681 - 168
110GLYGLYLEULEUBB1 - 1681 - 168
210GLYGLYLEULEULL1 - 1681 - 168
111SERSERPROPROCC0 - 3245 - 329
211SERSERPROPROEE0 - 3245 - 329
112SERSERPROPROCC0 - 3245 - 329
212SERSERPROPROGG0 - 3245 - 329
113SERSERPROPROCC0 - 3245 - 329
213SERSERPROPROII0 - 3245 - 329
114SERSERPROPROCC0 - 3245 - 329
214SERSERPROPROKK0 - 3245 - 329
115GLYGLYLEULEUDD1 - 1681 - 168
215GLYGLYLEULEUFF1 - 1681 - 168
116GLYGLYLEULEUDD1 - 1681 - 168
216GLYGLYLEULEUHH1 - 1681 - 168
117GLYGLYLEULEUDD1 - 1681 - 168
217GLYGLYLEULEUJJ1 - 1681 - 168
118GLYGLYLEULEUDD1 - 1681 - 168
218GLYGLYLEULEULL1 - 1681 - 168
119SERSERPROPROEE0 - 3245 - 329
219SERSERPROPROGG0 - 3245 - 329
120SERSERPROPROEE0 - 3245 - 329
220SERSERPROPROII0 - 3245 - 329
121SERSERPROPROEE0 - 3245 - 329
221SERSERPROPROKK0 - 3245 - 329
122GLYGLYLEULEUFF1 - 1681 - 168
222GLYGLYLEULEUHH1 - 1681 - 168
123GLYGLYLEULEUFF1 - 1681 - 168
223GLYGLYLEULEUJJ1 - 1681 - 168
124GLYGLYLEULEUFF1 - 1681 - 168
224GLYGLYLEULEULL1 - 1681 - 168
125SERSERPROPROGG0 - 3245 - 329
225SERSERPROPROII0 - 3245 - 329
126SERSERPROPROGG0 - 3245 - 329
226SERSERPROPROKK0 - 3245 - 329
127GLYGLYLEULEUHH1 - 1681 - 168
227GLYGLYLEULEUJJ1 - 1681 - 168
128GLYGLYLEULEUHH1 - 1681 - 168
228GLYGLYLEULEULL1 - 1681 - 168
129SERSERPROPROII0 - 3245 - 329
229SERSERPROPROKK0 - 3245 - 329
130GLYGLYLEULEUJJ1 - 1681 - 168
230GLYGLYLEULEULL1 - 1681 - 168

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: 37434.273 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: A/Taiwan/1/2013 influenza virus / Source: (gene. exp.) Influenza A virus / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0J9X246*PLUS
#2: Protein
Hemagglutinin HA2 chain


Mass: 20718.938 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: A/Taiwan/1/2013 influenza virus / Source: (gene. exp.) Influenza A virus / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0J9X245*PLUS
#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.: 18 / 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 744 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.48 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 8.5
Details: 0.01M nickel chloride, 0.1 M Tris-HCl, and 20% (w/v) PEG 2000MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 146479 / % possible obs: 96.6 % / Redundancy: 3.7 % / Net I/σ(I): 17.7

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementResolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.93 / SU B: 19.485 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.424 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25264 7372 5 %RANDOM
Rwork0.22184 ---
obs0.22336 139107 96.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å21.5 Å2
2---0.3 Å20 Å2
3----0.94 Å2
Refinement stepCycle: 1 / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23514 0 252 744 24510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01924354
X-RAY DIFFRACTIONr_bond_other_d0.0070.0222422
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.95233054
X-RAY DIFFRACTIONr_angle_other_deg1.287351570
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.73852946
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08124.8731182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.847154080
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3415120
X-RAY DIFFRACTIONr_chiral_restr0.0930.23576
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0227780
X-RAY DIFFRACTIONr_gen_planes_other0.0060.025688
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_it2.6312.87511820
X-RAY DIFFRACTIONr_mcbond_other2.6282.87411819
X-RAY DIFFRACTIONr_mcangle_it4.1544.30514754
X-RAY DIFFRACTIONr_mcangle_other4.1544.30514755
X-RAY DIFFRACTIONr_scbond_it3.723.33212534
X-RAY DIFFRACTIONr_scbond_other3.7193.33212535
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8454.82818301
X-RAY DIFFRACTIONr_long_range_B_refined9.38324.27127947
X-RAY DIFFRACTIONr_long_range_B_other9.38624.17927778
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)
11A192820.08
12C192820.08
21A193230.07
22E193230.07
31A194400.07
32G194400.07
41A191850.08
42I191850.08
51A193490.07
52K193490.07
61B86740.09
62D86740.09
71B82920.13
72F82920.13
81B85390.11
82H85390.11
91B86410.1
92J86410.1
101B85680.1
102L85680.1
111C194590.07
112E194590.07
121C194140.07
122G194140.07
131C193220.08
132I193220.08
141C192710.08
142K192710.08
151D83730.12
152F83730.12
161D86340.09
162H86340.09
171D86790.09
172J86790.09
181D86120.1
182L86120.1
191E195540.06
192G195540.06
201E193270.07
202I193270.07
211E192560.07
212K192560.07
221F84240.12
222H84240.12
231F83660.12
232J83660.12
241F83840.13
242L83840.13
251G192760.08
252I192760.08
261G193580.07
262K193580.07
271H85850.1
272J85850.1
281H87390.1
282L87390.1
291I192340.08
292K192340.08
301J86580.09
302L86580.09
LS refinement shellResolution: 2.402→2.465 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 449 -
Rwork0.316 8428 -
obs--79.74 %
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)
10.3269-0.0292-0.38690.08020.13420.6132-0.02670.0358-0.06580.0137-0.03160.03150.0818-0.05420.05830.23660.010.00360.1977-0.02450.15135.5516-126.2785-12.4711
21.06730.2706-1.56740.4457-0.17582.48140.10880.0136-0.06150.1051-0.22970.0724-0.1323-0.09520.1210.1637-0.07740.06270.2197-0.0670.108910.6128-118.163432.2818
30.43980.1159-0.51970.0565-0.12260.898-0.0985-0.1045-0.0758-0.0265-0.0214-0.04690.16340.06680.11990.25150.06440.04320.15040.05180.070660.9232-126.467100.3732
41.3654-0.3028-1.80680.19410.29912.49260.0244-0.0660.0011-0.06-0.009-0.02160.03480.0978-0.01530.22250.01850.05590.1485-0.01030.098986.4711-118.190555.8373
50.28140.0254-0.39580.0859-0.04860.56870.03790.10520.04070.04710.01240.0107-0.0455-0.1058-0.05030.22710.0460.01840.22930.04350.07538.8278-103.502986.0642
60.41150.036-0.67370.0581-0.23411.71770.05650.0730.0255-0.0067-0.01840.01020.0571-0.0362-0.03820.24930.0030.02220.22180.02330.088173.08-105.564247.4786
70.26990.0188-0.29010.11570.04270.36930.0746-0.11410.0064-0.0434-0.0555-0.0154-0.06270.1189-0.01910.2241-0.08090.03560.2228-0.03830.014357.7983-103.34441.8279
80.1908-0.0601-0.57360.04060.23862.26920.0853-0.09370.0421-0.0082-0.02830.00150.06060.0591-0.0570.2322-0.13530.05080.2197-0.0670.022123.7807-105.395840.6049
90.2139-0.0325-0.38210.14660.12480.73370.07570.0620.0477-0.0920.0010.0205-0.2229-0.1447-0.07670.31970.1420.06270.12150.03320.038230.0738-92.0847-16.0044
101.8127-0.4054-1.9750.17510.33312.37610.08340.0134-0.1160.0039-0.09690.0728-0.28340.06960.01350.31360.03940.10150.1214-0.03650.06527.7089-98.427430.4411
110.26490.0784-0.44090.2977-0.1630.77830.1207-0.09930.0270.1432-0.0519-0.0041-0.28320.2593-0.06880.2996-0.16330.04570.26-0.060.016166.5431-92.1746103.8698
121.43990.4231-1.49450.2326-0.3181.72080.0106-0.028-0.0409-0.04220.0393-0.0752-0.11350.041-0.04990.2305-0.07940.06470.1853-0.01170.112189.1822-98.487957.6411
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 402
2X-RAY DIFFRACTION2B1 - 168
3X-RAY DIFFRACTION3C0 - 402
4X-RAY DIFFRACTION4D1 - 168
5X-RAY DIFFRACTION5E0 - 402
6X-RAY DIFFRACTION6F1 - 168
7X-RAY DIFFRACTION7G0 - 402
8X-RAY DIFFRACTION8H1 - 168
9X-RAY DIFFRACTION9I0 - 402
10X-RAY DIFFRACTION10J1 - 168
11X-RAY DIFFRACTION11K0 - 402
12X-RAY DIFFRACTION12L1 - 168

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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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