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- PDB-2wrf: structure of H2 avian jena hemagglutinin with human receptor -

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Basic information

Entry
Database: PDB / ID: 2wrf
Titlestructure of H2 avian jena hemagglutinin with human receptor
ComponentsHEMAGGLUTININ
KeywordsVIRAL PROTEIN / GLYCOPROTEIN / LIPOPROTEIN / ENVELOPE PROTEIN
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 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
N-acetyl-alpha-neuraminic acid / Hemagglutinin
Similarity search - Component
Biological speciesINFLUENZA A VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.1 Å
AuthorsLiu, J. / Stevens, D.J. / Haire, L.F. / Walker, P.A. / Coombs, P.J. / Russell, R.J. / Gamblin, S.J. / Skehel, J.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: From the Cover: Structures of Receptor Complexes Formed by Hemagglutinins from the Asian Influenza Pandemic of 1957.
Authors: Liu, J. / Stevens, D.J. / Haire, L.F. / Walker, P.A. / Coombs, P.J. / Russell, R.J. / Gamblin, S.J. / Skehel, J.J.
History
DepositionSep 1, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / 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_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)516,31211
Polymers515,5319
Non-polymers7812
Water00
1
D: HEMAGGLUTININ
E: HEMAGGLUTININ
F: HEMAGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,6245
Polymers171,8443
Non-polymers7812
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15390 Å2
ΔGint-64.45 kcal/mol
Surface area57930 Å2
MethodPISA
2
A: HEMAGGLUTININ
B: HEMAGGLUTININ
C: HEMAGGLUTININ


Theoretical massNumber of molelcules
Total (without water)171,8443
Polymers171,8443
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14070 Å2
ΔGint-55.8 kcal/mol
Surface area58420 Å2
MethodPISA
3
G: HEMAGGLUTININ
H: HEMAGGLUTININ
I: HEMAGGLUTININ


Theoretical massNumber of molelcules
Total (without water)171,8443
Polymers171,8443
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13320 Å2
ΔGint-54.94 kcal/mol
Surface area59510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.173, 113.278, 184.668
Angle α, β, γ (deg.)90.00, 92.20, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
12
22
32
42
52
62
72

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN G AND (RESSEQ 7:323 )
211CHAIN B AND (RESSEQ 7:323 )
311CHAIN C AND (RESSEQ 7:323 )
411CHAIN E AND (RESSEQ 7:323 )
511CHAIN F AND (RESSEQ 7:323 )
611CHAIN H AND (RESSEQ 7:323 )
711CHAIN I AND (RESSEQ 7:323 )
112CHAIN D AND (RESSEQ 330:492 )
212CHAIN B AND (RESSEQ 330:492 )
312CHAIN C AND (RESSEQ 330:492 )
412CHAIN H AND (RESSEQ 330:492 )
512CHAIN I AND (RESSEQ 330:492 )
612CHAIN E AND (RESSEQ 330:492 )
712CHAIN F AND (RESSEQ 330:492 )

NCS ensembles :
ID
1
2

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Components

#1: Protein
HEMAGGLUTININ


Mass: 57281.270 Da / Num. of mol.: 9 / Fragment: RESIDUES 1-507 / Source method: isolated from a natural source
Source: (natural) INFLUENZA A VIRUS (A/CHICKEN/POTSDAM/4705/1984(H2N2))
References: UniProt: Q67326
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-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/a6-b2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.21 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. obs: 93242 / % possible obs: 99.6 % / Observed criterion σ(I): 2.1 / Redundancy: 3.8 % / Biso Wilson estimate: 62.74 Å2 / Rmerge(I) obs: 0.11

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 3.1→29.92 Å / SU ML: 2.59 / σ(F): 0.04 / Phase error: 36.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3368 4652 5 %
Rwork0.2733 --
obs0.2765 93242 92.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.215 Å2 / ksol: 0.256 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--17.2766 Å20 Å2-6.9535 Å2
2--24.8414 Å20 Å2
3----7.5648 Å2
Refinement stepCycle: LAST / Resolution: 3.1→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34524 0 53 0 34577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00835405
X-RAY DIFFRACTIONf_angle_d1.10547849
X-RAY DIFFRACTIONf_dihedral_angle_d18.5512817
X-RAY DIFFRACTIONf_chiral_restr0.0725126
X-RAY DIFFRACTIONf_plane_restr0.0046241
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11G2485X-RAY DIFFRACTIONPOSITIONAL
12B2485X-RAY DIFFRACTIONPOSITIONAL0.062
13C2485X-RAY DIFFRACTIONPOSITIONAL0.057
14E2485X-RAY DIFFRACTIONPOSITIONAL0.053
15F2485X-RAY DIFFRACTIONPOSITIONAL0.049
16H2485X-RAY DIFFRACTIONPOSITIONAL0.042
17I2485X-RAY DIFFRACTIONPOSITIONAL0.044
21D1303X-RAY DIFFRACTIONPOSITIONAL
22B1303X-RAY DIFFRACTIONPOSITIONAL0.036
23C1303X-RAY DIFFRACTIONPOSITIONAL0.033
24H1303X-RAY DIFFRACTIONPOSITIONAL0.051
25I1303X-RAY DIFFRACTIONPOSITIONAL0.046
26E1303X-RAY DIFFRACTIONPOSITIONAL0.03
27F1303X-RAY DIFFRACTIONPOSITIONAL0.027
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.13520.39171330.352546X-RAY DIFFRACTION80
3.1352-3.1720.35531050.34892606X-RAY DIFFRACTION83
3.172-3.21070.41821570.35442608X-RAY DIFFRACTION83
3.2107-3.25130.42291370.35652679X-RAY DIFFRACTION84
3.2513-3.2940.44551260.33492696X-RAY DIFFRACTION85
3.294-3.33910.40621450.32642743X-RAY DIFFRACTION87
3.3391-3.38670.35881550.33082790X-RAY DIFFRACTION88
3.3867-3.43720.37171610.3362799X-RAY DIFFRACTION88
3.4372-3.49080.39611390.32552852X-RAY DIFFRACTION91
3.4908-3.5480.3691600.31352916X-RAY DIFFRACTION92
3.548-3.6090.35861430.30242914X-RAY DIFFRACTION92
3.609-3.67460.33951640.2922926X-RAY DIFFRACTION93
3.6746-3.74510.31171600.28232940X-RAY DIFFRACTION93
3.7451-3.82140.36911670.28022957X-RAY DIFFRACTION94
3.8214-3.90430.36751660.27092991X-RAY DIFFRACTION94
3.9043-3.99490.31261580.25712959X-RAY DIFFRACTION94
3.9949-4.09460.32681550.2563025X-RAY DIFFRACTION95
4.0946-4.2050.31951630.24873037X-RAY DIFFRACTION96
4.205-4.32840.27391620.24223066X-RAY DIFFRACTION97
4.3284-4.46770.2981750.22783050X-RAY DIFFRACTION97
4.4677-4.62680.30471480.21763105X-RAY DIFFRACTION96
4.6268-4.81130.28781570.2163077X-RAY DIFFRACTION97
4.8113-5.02930.30771710.22633111X-RAY DIFFRACTION98
5.0293-5.29310.27881460.2183140X-RAY DIFFRACTION98
5.2931-5.62270.31971570.22313165X-RAY DIFFRACTION98
5.6227-6.05350.28991650.24773133X-RAY DIFFRACTION98
6.0535-6.65660.34061630.25333163X-RAY DIFFRACTION99
6.6566-7.6060.35861780.25523175X-RAY DIFFRACTION99
7.606-9.53110.27011550.22493214X-RAY DIFFRACTION99
9.5311-29.92130.32381810.28883207X-RAY DIFFRACTION97
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)
10.0045-0.0040.00340.098-0.05660.02470.03820.03730.02130.0410.0153-0.0908-0.03290.2303-00.1498-0.0007-0.07890.3221-0.11790.284155.8643-5.757873.5595
20.00640.00720.05610.1324-0.15750.0343-0.0109-0.0165-0.04950.0926-0.1132-0.0349-0.07670.233100.1595-0.0957-0.0570.29260.05980.104754.992710.694786.1757
30.01760.0225-0.00120.0053-0.12030.0236-0.0420.01510.04950.0335-0.08050.0103-0.16440.254900.1254-0.1058-0.01230.41510.04910.083257.354613.512465.6845
40.06520.04750.06370.18360.23820.26270.1196-0.3286-0.25110.0302-0.10250.02940.00380.3853-00.14050.0621-0.0459-0.375-0.02620.16773.7548-11.564266.3797
50.05870.0371-0.02060.2651-0.04680.1558-0.0289-0.04610.03710.0512-0.00020.0369-0.04380.008700.1852-0.0517-0.02480.1439-0.00980.16972.529515.125787.9105
60.03260.02880.00590.17-0.1292-0.03420.039-0.1155-0.1207-0.0689-0.07450.0164-0.70171.312800.06010.5141-0.0305-1.2617-0.03350.11456.28620.421254.3
70.05440.0107-0.0530.1750.10080.38790.0838-0.0540.0822-0.0277-0.05790.01840.0411-0.124200.16790.00090.0020.152-0.03630.11342.17536.673-11.9784
80.03860.0554-0.06430.21320.03040.26840.1099-0.2077-0.12410.0152-0.01970.049-0.28170.241800.3197-0.0060.06220.3904-0.06820.16696.691421.849218.1474
9-0.02920.09760.00210.2121-0.03040.2491-0.2033-0.1554-0.10770.1389-0.00920.04880.31910.205600.36650.10850.10840.31340.05940.17634.5347-12.165216.5563
100.01240.01-0.00250.0004-0.04270.0075-0.03380.0710.031-0.0449-0.06020.01890.1235-0.3159-00.116-0.073-0.01730.8574-0.11360.2141-48.74568.86621.6489
110.0079-0.0028-0.0270.02350.03280.0343-0.028-0.00380.042-0.0189-0.03620.0821-0.0933-0.175100.19790.07120.04620.5586-0.1130.25-45.979418.014920.3914
120.01690.0022-0.00090.046-0.00750.044-0.09670.00380.10210.1526-0.00390.10120.1955-0.2386-00.3048-0.14670.16660.6928-0.18580.3585-47.3139-2.324619.1874
130.00690.00740.00760.23790.1035-0.06210.01310.1025-0.0256-0.03140.10450.08950.174-0.65300.15270.10350.0354-1.1612-0.04550.1075-18.624159.573941.2613
140.04840.12940.03640.1879-0.07240.0664-0.14640.00940.08940.0283-0.11150.0293-0.19640.497400.04040.36510.1439-0.9142-0.4409-0.0868-16.606777.962651.1033
150.02360.02380.04610.11280.0910.09410.0058-0.162-0.07320.17250.17340.1520.0223-0.0311-00.22090.04470.0526-0.025-0.03110.0791-17.380360.006661.9967
160.01320.0019-0.07730.08460.205-0.17360.04350.1662-0.12330.00380.05290.04670.03330.68140-0.54030.88220.3778-0.4162-0.5608-0.079232.96249.138233.4535
170.03420.01330.05150.18780.0717-0.1848-0.125-0.03240.072-0.03680.0487-0.0185-0.02180.46-00.0806-0.02490.02470.089-0.07490.100935.967881.78645.4627
180.04020.00140.05170.0287-0.00520.19380.1783-0.0323-0.1640.1521-0.0475-0.07450.0038-0.03800.0960.0695-0.13670.125-0.06690.231434.80754.862868.0898
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 330:492
2X-RAY DIFFRACTION2CHAIN B AND RESID 330:492
3X-RAY DIFFRACTION3CHAIN C AND RESID 330:492
4X-RAY DIFFRACTION4CHAIN A AND RESID 9:323
5X-RAY DIFFRACTION5CHAIN B AND RESID 9:323
6X-RAY DIFFRACTION6CHAIN C AND RESID 9:323
7X-RAY DIFFRACTION7CHAIN D AND RESID 9:323
8X-RAY DIFFRACTION8CHAIN E AND RESID 9:323
9X-RAY DIFFRACTION9CHAIN F AND RESID 9:323
10X-RAY DIFFRACTION10CHAIN D AND RESID 330:492
11X-RAY DIFFRACTION11CHAIN E AND RESID 330:492
12X-RAY DIFFRACTION12CHAIN F AND RESID 330:492
13X-RAY DIFFRACTION13CHAIN G AND RESID 330:492
14X-RAY DIFFRACTION14CHAIN H AND RESID 330:492
15X-RAY DIFFRACTION15CHAIN I AND RESID 330:492
16X-RAY DIFFRACTION16CHAIN G AND RESID 9:323
17X-RAY DIFFRACTION17CHAIN H AND RESID 9:323
18X-RAY DIFFRACTION18CHAIN I AND RESID 9:323

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