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- PDB-5kan: Crystal structure of multidonor HV1-18-class broadly neutralizing... -

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Basic information

Entry
Database: PDB / ID: 5kan
TitleCrystal structure of multidonor HV1-18-class broadly neutralizing Influenza A antibody 16.g.07 in complex with A/Hong Kong/1-4-MA21-1/1968 (H3N2) Hemagglutinin
Components
  • (Hemagglutinin ...) x 2
  • 16.g.07 Heavy chain
  • 16.g.07 Light chain
KeywordsIMMUNE SYSTEM / Influenza / multidonor / H5 / universal influenza vaccine
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 / Immunoglobulins ...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 / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.785 Å
AuthorsJoyce, M.G. / Thomas, P.V. / Wheatley, A.K. / McDermott, A.B. / Mascola, J.R. / Kwong, P.D.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2016
Title: Vaccine-Induced Antibodies that Neutralize Group 1 and Group 2 Influenza A Viruses.
Authors: Joyce, M.G. / Wheatley, A.K. / Thomas, P.V. / Chuang, G.Y. / Soto, C. / Bailer, R.T. / Druz, A. / Georgiev, I.S. / Gillespie, R.A. / Kanekiyo, M. / Kong, W.P. / Leung, K. / Narpala, S.N. / ...Authors: Joyce, M.G. / Wheatley, A.K. / Thomas, P.V. / Chuang, G.Y. / Soto, C. / Bailer, R.T. / Druz, A. / Georgiev, I.S. / Gillespie, R.A. / Kanekiyo, M. / Kong, W.P. / Leung, K. / Narpala, S.N. / Prabhakaran, M.S. / Yang, E.S. / Zhang, B. / Zhang, Y. / Asokan, M. / Boyington, J.C. / Bylund, T. / Darko, S. / Lees, C.R. / Ransier, A. / Shen, C.H. / Wang, L. / Whittle, J.R. / Wu, X. / Yassine, H.M. / Santos, C. / Matsuoka, Y. / Tsybovsky, Y. / Baxa, U. / Mullikin, J.C. / Subbarao, K. / Douek, D.C. / Graham, B.S. / Koup, R.A. / Ledgerwood, J.E. / Roederer, M. / Shapiro, L. / Kwong, P.D. / Mascola, J.R. / McDermott, A.B.
History
DepositionJun 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / 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 / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Sep 27, 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
B: Hemagglutinin HA2
C: Hemagglutinin HA1
D: Hemagglutinin HA2
E: Hemagglutinin HA1
F: Hemagglutinin HA2
G: 16.g.07 Heavy chain
H: 16.g.07 Heavy chain
I: 16.g.07 Light chain
J: 16.g.07 Heavy chain
K: 16.g.07 Light chain
L: 16.g.07 Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,04129
Polymers310,28012
Non-polymers3,76117
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area52490 Å2
ΔGint-176 kcal/mol
Surface area117220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.847, 147.562, 209.786
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
31chain E
12chain B
22chain D
32chain F
13chain G
23chain H
33chain J
14chain I
24chain K
34chain L

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNLYSLYSchain AAA8 - 3261 - 319
21ASNASNLYSLYSchain CCC8 - 3261 - 319
31ASNASNLYSLYSchain EEE8 - 3261 - 319
12GLYGLYVALVALchain BBB4 - 1761 - 173
22GLYGLYLYSLYSchain DDD4 - 1741 - 171
32GLYGLYILEILEchain FFF4 - 1731 - 170
13GLNGLNCYSCYSchain GGG1 - 2311 - 231
23GLNGLNCYSCYSchain HHH1 - 2311 - 231
33GLNGLNCYSCYSchain JJJ1 - 2311 - 231
14ASPASPCYSCYSchain III1 - 2141 - 214
24ASPASPCYSCYSchain KKK1 - 2141 - 214
34ASPASPCYSCYSchain LLL1 - 2141 - 214

NCS ensembles :
ID
1
2
3
4

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Components

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Hemagglutinin ... , 2 types, 6 molecules ACEBDF

#1: Protein Hemagglutinin HA1


Mass: 35154.539 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Hong Kong/1/1968 H3N2)
Strain: A/Hong Kong/1/1968 H3N2 / Gene: HA / Production host: Homo sapiens (human) / References: UniProt: Q91MA7
#2: Protein Hemagglutinin HA2


Mass: 19980.070 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Hong Kong/1/1968 H3N2)
Strain: A/Hong Kong/1/1968 H3N2 / Gene: HA / Production host: Homo sapiens (human) / References: UniProt: Q91MA7

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Antibody , 2 types, 6 molecules GHJIKL

#3: Antibody 16.g.07 Heavy chain


Mass: 24957.084 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody 16.g.07 Light chain


Mass: 23335.080 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars / Non-polymers , 2 types, 165 molecules

#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 17
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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

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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: 3.21 Å3/Da / Density % sol: 61.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.010M Tris(2-carboxyethyl)phosphine HCl (TCEP) , 0.09 M 2-(N-morpholino)ethanesulfonic acid (MES), pH 6.0, 12% (w/v) PEG-6000

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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: Apr 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.78→50 Å / Num. obs: 83716 / % possible obs: 83.2 % / Redundancy: 4.1 % / Net I/σ(I): 14.05

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4lss, 5k9q

4lss

5k9q


Resolution: 2.785→40.673 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.46
RfactorNum. reflection% reflection
Rfree0.2427 4106 4.91 %
Rwork0.2176 --
obs0.2189 83699 83.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 241 Å2 / Biso mean: 71.5849 Å2 / Biso min: 16.15 Å2
Refinement stepCycle: final / Resolution: 2.785→40.673 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21758 0 238 148 22144
Biso mean--94.69 45.34 -
Num. residues----2806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00422517
X-RAY DIFFRACTIONf_angle_d0.97330567
X-RAY DIFFRACTIONf_chiral_restr0.0393446
X-RAY DIFFRACTIONf_plane_restr0.0033947
X-RAY DIFFRACTIONf_dihedral_angle_d13.7958169
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4495X-RAY DIFFRACTION8.279TORSIONAL
12C4495X-RAY DIFFRACTION8.279TORSIONAL
13E4495X-RAY DIFFRACTION8.279TORSIONAL
21B2501X-RAY DIFFRACTION8.279TORSIONAL
22D2501X-RAY DIFFRACTION8.279TORSIONAL
23F2501X-RAY DIFFRACTION8.279TORSIONAL
31G3182X-RAY DIFFRACTION8.279TORSIONAL
32H3182X-RAY DIFFRACTION8.279TORSIONAL
33J3182X-RAY DIFFRACTION8.279TORSIONAL
41I2948X-RAY DIFFRACTION8.279TORSIONAL
42K2948X-RAY DIFFRACTION8.279TORSIONAL
43L2948X-RAY DIFFRACTION8.279TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7846-2.81730.2971230.355753455716
2.8173-2.85170.405490.365987192027
2.8517-2.88770.3669450.32571070111533
2.8877-2.92570.3395580.32091367142541
2.9257-2.96580.3821790.32551595167449
2.9658-3.00820.3771080.30091927203559
3.0082-3.0530.32781020.30982233233568
3.053-3.10070.30751200.30262389250974
3.1007-3.15160.30281240.29062637276180
3.1516-3.20590.3171420.28472781292385
3.2059-3.26410.30921550.28782970312591
3.2641-3.32690.30291690.28263077324694
3.3269-3.39480.30071580.25863168332697
3.3948-3.46860.27952080.26193180338898
3.4686-3.54920.27811400.24443255339599
3.5492-3.63790.25491860.23683234342099
3.6379-3.73620.24022100.23732543464100
3.7362-3.84610.23731510.228832923443100
3.8461-3.97010.25751670.227232943461100
3.9701-4.11190.22111900.20232773467100
4.1119-4.27630.20541490.188433263475100
4.2763-4.47070.19411580.169933173475100
4.4707-4.70610.20491660.165432853451100
4.7061-5.00050.1971780.166433203498100
5.0005-5.38570.19441820.173433213503100
5.3857-5.92620.22711710.192933493520100
5.9262-6.78040.19231650.205933763541100
6.7804-8.52960.20921570.2134053562100
8.5296-40.67710.24611960.1913489368599
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)
16.77591.8276-1.39952.5557-0.59351.1-0.01932.1508-0.154-0.4260.0463-0.292-0.17150.23210.06370.3899-0.01310.02590.62170.02130.343740.66841.862-81.6655
26.08722.7675-0.24972.3926-0.53230.3958-0.24721.1456-0.575-0.47540.28820.3507-0.1746-0.14780.03280.6301-0.0155-0.12190.7174-0.19250.83090.2308-19.0835-84.5247
35.60950.7741-1.13051.91270.39250.76670.07620.2888-1.4043-0.06820.17750.35090.1177-0.1369-0.15710.6524-0.0931-0.24840.6318-0.17231.6651-26.143-35.4354-79.6517
44.60730.0864-0.68743.9181-0.2573.1605-0.01010.0944-0.5750.27950.28150.3998-0.9946-0.3635-0.28860.5634-0.0341-0.06820.71010.04011.4967-37.8816-28.5759-76.0521
55.28082.5748-1.03142.4658-0.87261.29680.1399-0.3265-1.08950.13660.07840.2850.2527-0.1061-0.34540.5749-0.1261-0.19430.65340.07541.6764-25.6051-34.8079-71.0253
64.68640.76680.26691.2936-0.74221.013-0.17090.6937-1.0795-0.28990.00420.20250.31830.01710.09020.5112-0.0891-0.04350.6946-0.28040.79481.7269-18.989-82.8227
74.654-0.2285-2.70610.4725-0.05661.61770.24620.21461.4783-0.086-0.02520.2704-0.1540.0688-0.04690.4197-0.0680.0030.5427-0.00440.537622.0639-0.6848-80.461
86.45591.79044.61956.63392.07554.2555-0.51051.36681.3359-1.21880.7144-0.4895-0.53140.83460.00260.5765-0.05620.0710.70130.05250.57840.70491.4592-82.3214
910.04851.815-4.51581.5689-1.59753.4537-0.13180.422-0.7173-0.04030.0956-0.3513-0.33260.0032-0.15430.42310.0209-0.00920.4306-0.03090.321539.5757-7.7471-77.3661
103.20781.8224-2.50873.1807-0.11192.22570.3373-0.7253-0.32970.563-0.28350.06550.2698-0.11210.37250.63270.0118-0.0020.5757-0.06851.16874.6383-21.1542-71.7265
114.771-2.0492-4.01355.51830.52513.75040.77120.2913-0.1743-1.0517-0.6122-0.11460.276-1.8411-0.04410.54680.0194-0.05890.9772-0.2130.877-15.4538-12.0019-77.6284
122.54670.1748-1.34490.3303-0.12110.55340.338-0.16680.2591-0.0372-0.18210.0743-0.05210.0853-0.00820.3523-0.0182-0.01430.4696-0.05120.430217.3234-4.0959-69.6415
135.5665-0.21651.76154.74471.82117.64-0.2154-0.0259-0.1061-0.02350.2687-0.2533-0.11240.3012-0.03930.2849-0.0540.03780.4532-0.04820.491158.38420.6522-71.4172
144.91481.2242-2.57241.1337-2.55936.05570.13810.12030.2878-0.8641-0.0877-0.4108-0.56970.62540.28631.12540.2718-0.07630.89560.04371.772567.669915.4783-67.1948
153.87640.52910.23510.6145-0.12530.20730.0711-0.4624-0.66440.1515-0.0503-0.11030.01320.1011-0.01450.50640.02760.0160.5051-0.01290.49039.65-18.3457-45.3207
169.82564.17965.33585.97740.60171.92110.4807-0.8396-0.14630.3582-0.16230.8215-0.0167-0.2138-0.08660.51340.02480.05810.48120.06180.5751-21.6949-24.3486-42.5544
175.1550.74441.10373.84370.01292.59420.0201-0.8271-0.35680.34960.06580.8147-0.1723-0.2268-0.12170.42860.10660.07420.56180.20280.6845-38.2956-19.8167-43.3752
182.8146-1.10471.37026.82660.58941.99470.10940.1287-0.199-0.75070.1014-0.2683-0.20050.0911-0.18580.591-0.0544-0.05730.53080.23570.898-39.6513-23.4732-54.295
194.7832-1.66481.24452.7915-0.52792.5721-0.1016-0.5651-0.0213-0.02890.22910.4714-0.43470.0122-0.10030.46860.04840.01270.46950.09770.5383-33.5984-12.8171-46.6126
206.77421.8868-3.13375.1458-2.29971.52920.0652-0.2355-0.08280.19010.1491-0.0665-0.25710.1035-0.14450.4403-0.0303-0.00890.5362-0.05940.3556-0.3537-18.8274-44.657
215.85520.64470.86023.05741.10461.9250.69651.3645-0.80430.6621-0.1553-0.47870.68970.5922-0.03820.47640.092-0.090.57140.00710.452725.4634-16.5351-53.8972
227.47691.87190.45722.0114-0.05380.62620.2879-0.085-0.55550.0579-0.2089-0.41980.23240.2726-0.0880.5150.0675-0.03010.632-0.01220.446938.9854-7.0406-45.6402
234.07263.44082.0482.99251.81640.96320.14640.54561.13670.54590.36710.7345-0.4977-0.58830.00930.7556-0.0490.00461.1897-0.0540.9099-0.6462-7.7007-47.5903
246.49561.65431.04395.07790.81913.69230.24090.7244-1.07660.0906-0.33411.15790.7412-0.7145-0.03611.0646-0.0334-0.13110.84160.02591.0532-13.1558-23.2927-58.683
258.77052.12563.51671.11980.89081.73950.03050.21550.17820.16110.01370.05410.14510.16540.02750.39720.0018-0.01710.4468-0.04770.437417.7801-7.6426-58.3197
267.45771.8728-0.44365.5956-1.38931.1476-0.0709-0.38030.1371-0.0603-0.084-0.5841-0.4360.32740.13470.5102-0.0131-0.12770.6965-0.13260.589557.19164.7194-48.7596
275.6165.6601-2.51854.7718-2.44520.78940.4062-1.73860.96550.0433-0.2294-0.0965-0.04630.1036-0.07990.4368-0.08170.03110.5801-0.27010.703233.341621.719-54.1655
287.05461.17531.31350.16230.29620.7477-0.22810.22650.88740.08410.07740.1666-0.1344-0.03950.15540.47580.0071-0.00760.47590.00620.6344-17.449111.5872-64.8248
295.56971.72560.58793.1208-0.71491.8616-0.0510.6519-0.0045-0.09740.04390.1134-0.0722-0.0566-0.00880.38530.0364-0.03060.5203-0.00460.497-42.24590.1087-76.8416
309.9245-1.4449-1.98546.65920.9123.1691-0.1155-0.3404-0.92350.34120.3780.07110.73920.7178-0.24130.45080.0284-0.0630.49070.0240.6245-43.0667-8.8193-69.5146
315.20660.52060.6752.94080.03761.8577-0.06060.8064-0.5212-0.1552-0.0862-0.2951-0.02780.44860.05940.3830.0445-0.00470.6564-0.11490.5371-34.2236-3.0604-79.5509
323.02580.0971-0.64821.6453-0.0362.06380.0530.23060.7329-0.1694-0.020.1473-0.1372-0.05470.04440.4059-0.0035-0.04120.5083-0.01280.5839-8.828612.5585-64.2001
337.07746.6005-0.64847.75060.54961.05730.8782-0.4735-0.02860.9921-0.3827-0.3412-0.18110.4121-0.12310.4998-0.0559-0.030.5459-0.03540.461116.276413.391-53.6543
347.78642.3530.51013.19270.09560.7214-0.0991-0.47481.12510.28550.1857-0.1648-0.06730.069-0.0390.437-0.0062-0.06720.4748-0.1430.710831.078421.7532-60.9175
352.608-0.15071.51173.07512.3912.41470.05561.1392-0.00580.317-0.13830.5135-0.4975-0.30330.33990.63580.0149-0.01790.56890.08340.7622-11.17371.9974-65.6039
369.44114.91980.50763.68170.51590.4885-0.1065-0.1191-0.561-0.02520.117-0.376-0.00880.0241-0.0630.3829-0.0354-0.02120.4227-0.01690.397414.58773.385-60.9112
377.1645-0.0484-2.37152.8975-1.08083.9554-0.0441-0.13710.9985-0.14630.0249-0.3873-0.0960.51970.11160.4825-0.1032-0.00160.4882-0.15830.789152.486921.6725-62.7686
383.3579-0.39110.47368.83384.15283.36850.1766-0.6022-0.18140.92120.2521-0.99430.31350.6377-0.06210.65040.0288-0.04420.8898-0.00760.563328.82513.0508-18.5288
394.34431.8389-0.27562.83322.88395.6610.1748-0.22650.41650.2065-0.0765-0.1809-0.43370.4396-0.19440.5182-0.03920.00080.56620.03450.466225.713210.0441-25.0185
40-0.1969-0.8888-1.27934.31284.80649.6684-0.0464-0.0533-0.00010.5999-0.0177-0.0147-0.1204-0.0695-0.01750.60920.0002-0.00650.64940.04410.524315.08819.1498-14.2371
415.90092.10530.35794.46840.98455.21130.0283-0.1798-0.01460.61620.1145-0.121-0.40670.3922-0.15410.96140.0229-0.08170.65260.05860.49657.658717.86718.1341
423.5728-1.54761.35976.2005-1.39670.69660.43640.92930.103-0.8494-0.4152-0.60640.10961.2079-0.09590.69130.02770.17010.6149-0.15850.556245.2182-41.1825-82.6568
433.346-2.6462.15997.2741-2.70323.12880.30090.2874-0.7394-0.6871-0.0825-0.4144-0.35990.28480.1280.5467-0.00580.13080.4582-0.03650.656740.3867-28.0072-85.5318
446.06213.0904-1.43172.1296-0.19931.5406-0.3891-0.0773-1.16290.49410.449-0.27070.17310.03130.13180.5453-0.04270.0240.44860.04990.572336.095-40.0071-74.5716
456.55443.1057-0.49512.3440.86162.95170.0371-0.7901-0.18390.6939-0.1573-0.32440.17650.3573-0.08680.53370.05930.02220.48560.02450.445639.0456-28.8852-71.3686
466.7761-0.0274-0.73058.08420.89063.66750.0933-0.03770.06670.43070.0042-0.6476-1.13350.046-0.10470.48990.0071-0.00730.52020.02790.735646.8385-30.7853-77.1096
473.6265-1.6528-0.34548.11111.1740.70920.0302-0.4455-0.58740.76820.0081-0.94170.17250.10630.040.4037-0.0149-0.0920.48840.08310.712241.5274-40.3581-73.9771
482.2617-0.6431-0.14848.5144-0.09190.7670.14370.283-0.1489-0.6089-0.40230.0188-0.09040.29120.1540.4477-0.03390.04810.4334-0.03480.350829.0177-25.5772-80.3746
491.1264-2.84580.2338.56122.35856.60420.53210.2251-0.2342-0.2414-0.5536-0.29320.9706-0.2405-0.18650.6967-0.05820.17320.78450.01490.547639.6491-64.1556-88.3433
503.92121.068-0.45914.70640.57373.1972-0.1920.78840.1321-0.77920.1501-0.38440.24-0.0652-0.06910.7169-0.04360.21990.68660.01480.642635.2445-62.0808-91.8593
518.70231.62560.2754.14073.51437.8213-0.05620.8003-0.5481-0.9178-0.4032-0.52820.54880.3073-0.01441.1562-0.03590.38881.0652-0.02070.972242.2009-64.2457-97.6702
527.491.8678-0.92772.15691.08832.43150.16160.20040.1187-0.04680.04750.2985-0.7241-0.7046-0.00580.62450.17920.08730.51210.06080.5246-0.74837.1859-27.3443
535.91520.17941.63922.12321.63535.78810.1541.1851-0.50620.16350.05290.2702-0.4437-0.1919-0.48550.42570.12380.05440.5633-0.05090.4588.91312.8605-34.2312
548.6895-0.5012-2.76734.29233.91013.7314-0.2291-0.4299-0.99420.77190.32090.25450.4272-0.5717-0.10540.6110.08060.00160.5610.14650.43677.703-4.7911-24.0558
557.92324.9907-5.15945.7786-4.29949.2509-0.59250.5532-0.2509-0.41510.67-0.01970.0986-0.1738-0.14960.42050.0910.06260.598-0.00040.51680.33140.2113-33.4434
567.35533.4881-2.78973.1816-0.32932.4343-0.266-1.5567-0.76940.0244-0.3307-0.17670.81530.84030.0820.55970.17020.01150.64170.2060.51722.61530.6696-21.3998
572.1747-0.8699-0.34950.75811.69362.15990.1910.71520.11830.0954-0.0438-0.1258-0.074-1.1819-0.20150.56830.08860.04480.71070.09930.51213.59968.9207-22.835
587.25992.69750.8898.92090.05162.36040.29490.07960.4691.1453-0.1918-0.8073-1.28720.2462-0.04361.78140.1885-0.23950.8739-0.04410.60833.05929.74768.2516
593.20232.59881.82032.48231.26221.2589-0.09520.3750.4324-0.2946-0.27120.1167-1.02920.1644-0.07671.28990.0206-0.10290.85340.12040.5666-3.884324.1718-4.2962
601.6050.48980.06595.41523.58432.78260.26790.45340.9786-0.78080.22890.6933-1.6523-1.5951-0.05621.5930.16940.16211.07120.36640.86770.048932.475-6.2993
613.24842.63090.81697.20974.22383.8274-0.031-0.17160.37690.37220.01490.0242-1.1843-0.1249-0.01811.32240.1406-0.0020.84120.22690.499-1.037726.521-1.0877
625.93744.68883.62815.07225.97318.8051-0.271-0.43931.14770.4055-1.03731.7877-1.1072-0.72690.53151.27530.1585-0.10121.14990.10370.905-10.946429.41741.2262
634.2888-0.6656-0.49034.4215-2.88193.4790.18250.3681.0577-0.1950.2122-0.2938-2.08320.5641-0.34421.0769-0.2182-0.071.0280.23280.97720.357740.5375-90.8471
643.7162-0.3197-1.68675.61131.23347.54810.38660.4410.49470.71340.3331-0.2601-1.21590.3716-0.29650.5808-0.06670.01670.5230.1151.08621.14735.7473-78.5255
655.3566-0.38760.50726.8419-0.53687.8295-0.41941.35060.8074-0.91680.06930.1046-0.6083-0.59770.01590.6477-0.1401-0.23220.94360.22770.658115.752529.3966-92.3629
666.08890.10511.56485.8023-0.76849.63780.32611.2279-0.3508-0.54020.3806-0.88960.64621.1077-0.42550.5257-0.0178-0.0130.63090.04030.672423.506923.9331-85.0752
674.45130.041-0.05346.8318-0.82796.9488-0.35820.60430.7162-0.46430.15610.1561-0.79271.1150.14110.5989-0.2201-0.0430.92080.20511.005828.150232.566-85.9238
681.26421.2309-2.00741.9843-3.32816.5582-0.21320.8525-0.0275-1.08190.95850.96070.44820.207-0.15650.7564-0.3057-0.01311.08170.18060.924419.723131.8779-94.9613
692.251-2.2683.02952.9744-2.83867.66570.0064-0.0660.20880.2910.85620.2993-0.5676-0.3664-0.43780.4515-0.0652-0.06390.52730.11940.795213.323825.5727-76.0897
702.8022-1.9160.97395.3574-2.23894.3274-0.27621.58571.4302-1.4379-0.24010.2439-1.62370.68550.46021.6262-0.5443-0.17991.49690.49291.253420.627943.1063-104.5677
712.19-2.77292.75222.5904-2.23225.2738-0.84940.76050.36950.8325-0.22810.7178-0.63990.3645-0.85961.5704-0.1912-0.44951.93120.83462.19780.970850.1329-111.8542
722.08730.6882.3913.4902-1.65194.39170.35580.44680.7318-1.1733-0.05250.8854-0.8120.2849-0.12341.3733-0.1071-0.24011.660.71451.82875.080743.2599-108.3233
731.67131.8591-1.92312.7754-1.64032.78870.73840.04550.7375-0.2898-0.6361-0.6088-1.65520.29130.08551.9496-0.2481-0.32612.06841.12832.8218-4.332454.2284-109.1297
743.16920.73281.2862.7845-2.80914.3902-0.28990.70590.3851-0.83470.5173-0.4105-0.1572-0.78360.04021.9831-0.2033-0.50751.76910.60442.45815.033357.3367-111.1966
752.40521.45490.76982.3314-0.60434.55310.14510.72370.3011-0.48990.38290.53630.4233-1.0425-0.20850.719-0.2173-0.22630.9820.32640.84351.944620.2208-87.675
760.2402-0.44741.0341.9579-0.31472.4449-0.46570.90640.7125-1.45260.96560.72080.4641-0.36893.5321.6982-0.4636-0.4982.20.77661.3355-2.106138.3685-119.6584
774.55920.1856-1.04266.81842.61183.57660.298-1.0697-0.07170.6496-0.42040.56140.3255-0.15060.02220.7228-0.01610.0870.60930.01960.570421.8901-41.2037-65.1075
788.25381.32215.24155.77554.25785.3821-0.4684-0.7098-0.33620.4884-0.6841.55630.5367-1.39220.23470.6537-0.06950.31710.5307-0.03020.838111.6156-44.1742-71.9325
794.32460.55790.12482.5997-0.98821.5732-0.0136-0.1879-0.16970.66860.22890.462-0.2480.5229-0.12120.45690.00640.02570.4535-0.04460.411821.3882-31.3139-70.7881
803.77910.8158-0.03035.1649-3.38152.3293-0.19530.3963-0.8295-0.4633-0.03270.95920.459-0.51160.00320.5918-0.0621-0.04270.5028-0.13990.564819.6019-36.7993-82.1147
810.82191.30662.07378.6516.55037.5744-0.0017-0.34810.14930.7586-0.35480.63680.4456-0.6371-0.05750.42190.02160.160.5616-0.11410.966813.0689-34.7587-71.3349
821.69930.6179-1.16674.3255-1.88421.0974-0.322-0.1934-0.4613-0.7096-0.34260.66870.2829-0.37430.17190.4959-0.03350.07880.5399-0.13250.582718.6299-43.6112-77.8843
83-0.08212.62761.11525.7923-0.10580.1986-0.1210.0299-0.005-0.34470.0636-0.40650.1920.02180.07450.5487-0.01950.15080.5907-0.14520.529829.0847-57.7337-80.8709
847.9342-5.658-0.17136.82740.73421.1455-0.08650.5173-0.66880.4794-0.02760.2322-0.19490.2248-0.08430.6006-0.0660.00310.5484-0.11470.348626.9852-71.8798-81.1762
852.2023-0.30690.8967.37350.10062.30810.03060.2259-0.51871.1405-0.0746-0.84960.5068-0.4935-0.25680.7033-0.18170.10020.6926-0.09830.599733.7509-76.8952-77.0076
864.6467-3.06661.16276.94081.132.6386-0.25720.017-0.0607-0.0230.3317-0.36660.2549-0.0861-0.04430.5169-0.14160.1140.54830.01690.571530.2417-67.535-83.3763
877.7445-5.0654-0.47846.62961.61831.744-0.08470.0931-1.2409-0.54370.177-0.3099-0.04280.5395-0.07430.88480.01270.06990.4984-0.15140.766533.3055-83.569-83.4855
884.3331-4.5546-2.15915.34980.64383.2598-0.00911.1446-0.96550.2096-0.23060.55230.46670.1891-0.10210.8002-0.00040.10980.7204-0.22290.675724.5296-80.7245-86.2288
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 26 )A8 - 26
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 79 )A27 - 79
3X-RAY DIFFRACTION3chain 'A' and (resid 80 through 175 )A80 - 175
4X-RAY DIFFRACTION4chain 'A' and (resid 176 through 228 )A176 - 228
5X-RAY DIFFRACTION5chain 'A' and (resid 229 through 265 )A229 - 265
6X-RAY DIFFRACTION6chain 'A' and (resid 266 through 308 )A266 - 308
7X-RAY DIFFRACTION7chain 'A' and (resid 309 through 326 )A309 - 326
8X-RAY DIFFRACTION8chain 'B' and (resid 4 through 21 )B4 - 21
9X-RAY DIFFRACTION9chain 'B' and (resid 22 through 55 )B22 - 55
10X-RAY DIFFRACTION10chain 'B' and (resid 56 through 65 )B56 - 65
11X-RAY DIFFRACTION11chain 'B' and (resid 66 through 75 )B66 - 75
12X-RAY DIFFRACTION12chain 'B' and (resid 76 through 126 )B76 - 126
13X-RAY DIFFRACTION13chain 'B' and (resid 127 through 170 )B127 - 170
14X-RAY DIFFRACTION14chain 'B' and (resid 171 through 176 )B171 - 176
15X-RAY DIFFRACTION15chain 'C' and (resid 8 through 79 )C8 - 79
16X-RAY DIFFRACTION16chain 'C' and (resid 80 through 104 )C80 - 104
17X-RAY DIFFRACTION17chain 'C' and (resid 105 through 195 )C105 - 195
18X-RAY DIFFRACTION18chain 'C' and (resid 196 through 228 )C196 - 228
19X-RAY DIFFRACTION19chain 'C' and (resid 229 through 265 )C229 - 265
20X-RAY DIFFRACTION20chain 'C' and (resid 266 through 308 )C266 - 308
21X-RAY DIFFRACTION21chain 'C' and (resid 309 through 326 )C309 - 326
22X-RAY DIFFRACTION22chain 'D' and (resid 4 through 55 )D4 - 55
23X-RAY DIFFRACTION23chain 'D' and (resid 56 through 65 )D56 - 65
24X-RAY DIFFRACTION24chain 'D' and (resid 66 through 75 )D66 - 75
25X-RAY DIFFRACTION25chain 'D' and (resid 76 through 126 )D76 - 126
26X-RAY DIFFRACTION26chain 'D' and (resid 127 through 174 )D127 - 174
27X-RAY DIFFRACTION27chain 'E' and (resid 8 through 26 )E8 - 26
28X-RAY DIFFRACTION28chain 'E' and (resid 27 through 104 )E27 - 104
29X-RAY DIFFRACTION29chain 'E' and (resid 105 through 195 )E105 - 195
30X-RAY DIFFRACTION30chain 'E' and (resid 196 through 228 )E196 - 228
31X-RAY DIFFRACTION31chain 'E' and (resid 229 through 265 )E229 - 265
32X-RAY DIFFRACTION32chain 'E' and (resid 266 through 308 )E266 - 308
33X-RAY DIFFRACTION33chain 'E' and (resid 309 through 326 )E309 - 326
34X-RAY DIFFRACTION34chain 'F' and (resid 4 through 55 )F4 - 55
35X-RAY DIFFRACTION35chain 'F' and (resid 56 through 75 )F56 - 75
36X-RAY DIFFRACTION36chain 'F' and (resid 76 through 126 )F76 - 126
37X-RAY DIFFRACTION37chain 'F' and (resid 127 through 173 )F127 - 173
38X-RAY DIFFRACTION38chain 'G' and (resid 1 through 32 )G1 - 32
39X-RAY DIFFRACTION39chain 'G' and (resid 33 through 98 )G33 - 98
40X-RAY DIFFRACTION40chain 'G' and (resid 99 through 149 )G99 - 149
41X-RAY DIFFRACTION41chain 'G' and (resid 150 through 231 )G150 - 231
42X-RAY DIFFRACTION42chain 'H' and (resid 1 through 17 )H1 - 17
43X-RAY DIFFRACTION43chain 'H' and (resid 18 through 32 )H18 - 32
44X-RAY DIFFRACTION44chain 'H' and (resid 33 through 44 )H33 - 44
45X-RAY DIFFRACTION45chain 'H' and (resid 45 through 64 )H45 - 64
46X-RAY DIFFRACTION46chain 'H' and (resid 65 through 83 )H65 - 83
47X-RAY DIFFRACTION47chain 'H' and (resid 84 through 99 )H84 - 99
48X-RAY DIFFRACTION48chain 'H' and (resid 100 through 121 )H100 - 121
49X-RAY DIFFRACTION49chain 'H' and (resid 122 through 149 )H122 - 149
50X-RAY DIFFRACTION50chain 'H' and (resid 150 through 215 )H150 - 215
51X-RAY DIFFRACTION51chain 'H' and (resid 216 through 231 )H216 - 231
52X-RAY DIFFRACTION52chain 'I' and (resid 1 through 25 )I1 - 25
53X-RAY DIFFRACTION53chain 'I' and (resid 26 through 38 )I26 - 38
54X-RAY DIFFRACTION54chain 'I' and (resid 39 through 61 )I39 - 61
55X-RAY DIFFRACTION55chain 'I' and (resid 62 through 75 )I62 - 75
56X-RAY DIFFRACTION56chain 'I' and (resid 76 through 90 )I76 - 90
57X-RAY DIFFRACTION57chain 'I' and (resid 91 through 113 )I91 - 113
58X-RAY DIFFRACTION58chain 'I' and (resid 114 through 128 )I114 - 128
59X-RAY DIFFRACTION59chain 'I' and (resid 129 through 150 )I129 - 150
60X-RAY DIFFRACTION60chain 'I' and (resid 151 through 163 )I151 - 163
61X-RAY DIFFRACTION61chain 'I' and (resid 164 through 197 )I164 - 197
62X-RAY DIFFRACTION62chain 'I' and (resid 198 through 214 )I198 - 214
63X-RAY DIFFRACTION63chain 'J' and (resid 1 through 16 )J1 - 16
64X-RAY DIFFRACTION64chain 'J' and (resid 17 through 32 )J17 - 32
65X-RAY DIFFRACTION65chain 'J' and (resid 33 through 44 )J33 - 44
66X-RAY DIFFRACTION66chain 'J' and (resid 45 through 64 )J45 - 64
67X-RAY DIFFRACTION67chain 'J' and (resid 65 through 84 )J65 - 84
68X-RAY DIFFRACTION68chain 'J' and (resid 85 through 98 )J85 - 98
69X-RAY DIFFRACTION69chain 'J' and (resid 99 through 121 )J99 - 121
70X-RAY DIFFRACTION70chain 'J' and (resid 122 through 134 )J122 - 134
71X-RAY DIFFRACTION71chain 'J' and (resid 135 through 172 )J135 - 172
72X-RAY DIFFRACTION72chain 'J' and (resid 173 through 192 )J173 - 192
73X-RAY DIFFRACTION73chain 'J' and (resid 193 through 215 )J193 - 215
74X-RAY DIFFRACTION74chain 'J' and (resid 216 through 231 )J216 - 231
75X-RAY DIFFRACTION75chain 'K' and (resid 1 through 102 )K1 - 102
76X-RAY DIFFRACTION76chain 'K' and (resid 103 through 214 )K103 - 214
77X-RAY DIFFRACTION77chain 'L' and (resid 1 through 12 )L1 - 12
78X-RAY DIFFRACTION78chain 'L' and (resid 13 through 25 )L13 - 25
79X-RAY DIFFRACTION79chain 'L' and (resid 26 through 38 )L26 - 38
80X-RAY DIFFRACTION80chain 'L' and (resid 39 through 61 )L39 - 61
81X-RAY DIFFRACTION81chain 'L' and (resid 62 through 75 )L62 - 75
82X-RAY DIFFRACTION82chain 'L' and (resid 76 through 90 )L76 - 90
83X-RAY DIFFRACTION83chain 'L' and (resid 91 through 128 )L91 - 128
84X-RAY DIFFRACTION84chain 'L' and (resid 129 through 150 )L129 - 150
85X-RAY DIFFRACTION85chain 'L' and (resid 151 through 163 )L151 - 163
86X-RAY DIFFRACTION86chain 'L' and (resid 164 through 186 )L164 - 186
87X-RAY DIFFRACTION87chain 'L' and (resid 187 through 197 )L187 - 197
88X-RAY DIFFRACTION88chain 'L' and (resid 198 through 214 )L198 - 214

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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

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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

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