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- PDB-4bgz: Crystal Structure of H5 (tyTy) Influenza Virus Haemagglutinin -

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Basic information

Entry
Database: PDB / ID: 4bgz
TitleCrystal Structure of H5 (tyTy) Influenza Virus Haemagglutinin
Components
  • HAEMAGGLUTININ HA1
  • HEMAGGLUTININ
KeywordsVIRAL PROTEIN / N-GLYCOSYLATION / VIRUS RECEPTOR / BIRD FLU
Function / homology
Function and homology information


viral budding from plasma membrane / 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 / 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
PHOSPHATE ION / Hemagglutinin
Similarity search - Component
Biological speciesINFLUENZA VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsXiong, X. / Coombs, P. / Martin, S.R. / Liu, J. / Xiao, H. / McCauley, J.W. / Locher, K. / Walker, P.A. / Collins, P.J. / Kawaoka, Y. ...Xiong, X. / Coombs, P. / Martin, S.R. / Liu, J. / Xiao, H. / McCauley, J.W. / Locher, K. / Walker, P.A. / Collins, P.J. / Kawaoka, Y. / Skehel, J.J. / Gamblin, S.J.
CitationJournal: Nature / Year: 2013
Title: Receptor Binding by a Ferret-Transmissible H5 Avian Influenza Virus.
Authors: Xiong, X. / Coombs, P. / R Martin, S. / Liu, J. / Xiao, H. / Mccauley, J.W. / Locher, K. / Walker, P.A. / Collins, P.J. / Kawaoka, Y. / Skehel, J.J. / Gamblin, S.J.
History
DepositionMar 29, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Database references
Revision 1.2May 15, 2013Group: Database references
Revision 1.3May 22, 2013Group: Database references
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
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: HAEMAGGLUTININ HA1
C: HEMAGGLUTININ
D: HAEMAGGLUTININ HA1
E: HEMAGGLUTININ
F: HAEMAGGLUTININ HA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,57914
Polymers168,3146
Non-polymers1,2658
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25800 Å2
ΔGint-137.9 kcal/mol
Surface area59960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.482, 228.492, 71.324
Angle α, β, γ (deg.)90.00, 113.88, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13C
23E
14B
24D
15B
25F
16D
26F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 319
2010C1 - 319
1020A1 - 318
2020E1 - 318
1030C1 - 318
2030E1 - 318
1040B10 - 154
2040D10 - 154
1050B10 - 153
2050F10 - 153
1060D10 - 153
2060F10 - 153

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein HEMAGGLUTININ / / HAEMAGGLUTININ HA1


Mass: 36978.715 Da / Num. of mol.: 3 / Fragment: HA1 TRYPSIN RELEASED ECTODOMAIN, RESIDUES 17-338
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA VIRUS / Strain: A/TURKEY/TURKEY/1/2005(H5N1) / Plasmid: PACGP67A / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q207Z6
#2: Protein HAEMAGGLUTININ HA1


Mass: 19126.004 Da / Num. of mol.: 3 / Fragment: HA2 TRYPSIN RELEASED ECTODOMAIN, RESIDUES 347-512
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA VIRUS / Strain: A/TURKEY/TURKEY/1/2005 (H5N1) / Plasmid: PACGP67A / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q207Z6
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMULTIBASIC SITE REMOVED

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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: 3.13 Å3/Da / Density % sol: 60.65 % / Description: NONE
Crystal growDetails: BIS-TRIS PROPANE PH 7.5, 0.05 - 0.15 M K/NAPO4 (PH 7.0), 15-18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.68→114.2 Å / Num. obs: 57647 / % possible obs: 100 % / Observed criterion σ(I): 2.1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10
Reflection shellResolution: 2.68→2.82 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.68→114.25 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.9 / SU B: 26.205 / SU ML: 0.285 / Cross valid method: THROUGHOUT / ESU R: 0.668 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.24392 2926 5.1 %RANDOM
Rwork0.21388 ---
obs0.21544 54721 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 95.428 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å2-1.05 Å2
2--6.89 Å20 Å2
3----3.94 Å2
Refinement stepCycle: LAST / Resolution: 2.68→114.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11016 0 76 398 11490
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01911353
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210413
X-RAY DIFFRACTIONr_angle_refined_deg1.0421.93915413
X-RAY DIFFRACTIONr_angle_other_deg0.7813.00323869
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.12651390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.34125.185569
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.914151886
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3731552
X-RAY DIFFRACTIONr_chiral_restr0.0560.21664
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213111
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022693
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_it0.862.7485578
X-RAY DIFFRACTIONr_mcbond_other0.862.7485577
X-RAY DIFFRACTIONr_mcangle_it1.54.1226962
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.0942.8865775
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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)
11A193760.06
12C193760.06
21A193500.05
22E193500.05
31C193380.06
32E193380.06
41B68020.08
42D68020.08
51B66480.1
52F66480.1
61D67600.11
62F67600.11
LS refinement shellResolution: 2.68→2.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 198 -
Rwork0.354 4091 -
obs--100 %
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)
10.4884-0.4281-1.935718.215710.428312.4546-0.28270.1476-0.4607-0.982-0.2071-0.89680.9321-0.57640.48981.68130.20230.07560.3173-0.28261.647215.9938-54.3284-25.3027
22.55460.3144-0.17263.1340.76342.1503-0.1336-0.3051-0.1539-0.1110.3124-0.36530.1210.6199-0.17880.04390.07090.03880.602-0.04280.095834.1156-1.4565-9.5758
30.380.2306-0.0070.14370.00970.0754-0.84050.3594-0.1399-0.55780.4409-0.07460.17760.14880.39963.4477-0.04840.22041.3922-0.46961.677815.323-50.733-34.7334
40.83522.66971.416918.7489.63137.87110.1062-0.0636-0.59330.694-0.0152-1.3541.43630.7635-0.09110.44570.24810.1980.2860.1980.603515.7569-16.7457-6.711
55.34937.80728.272212.390312.609913.76620.63110.4829-0.00780.6008-0.38050.87771.2972-0.2253-0.25052.24430.03470.00841.3476-0.59161.76356.9197-51.1231-30.3065
61.1518-0.1010.29020.015-0.01570.090.06360.38380.48070.0716-0.1047-0.07390.0955-0.01340.04112.7263-0.21660.18522.0904-0.4021.6465.9768-70.4904-44.9203
712.38361.16391.7984.24752.95182.72990.31690.0948-1.6182-1.2335-0.18950.41870.3186-0.7416-0.12743.0007-0.5854-0.69391.693-0.43641.4871-6.2891-39.1826-41.1485
82.02390.71830.87182.65991.71674.5727-0.07690.43170.2149-0.4598-0.0250.2075-0.601-0.25970.10190.13670.0983-0.05850.27590.03410.14670.246111.4086-13.4717
91.8343-0.0725-0.19010.0462-0.02680.06130.18170.1477-0.9785-0.0921-0.08020.30720.23850.0452-0.10152.7626-0.2892-0.57142.1021-0.55262.1869-14.9472-40.7079-35.7433
106.08316.62733.875512.09017.62826.4555-0.46320.6169-0.0524-0.6930.22890.40990.20850.30460.23430.29560.0562-0.02820.243-0.04150.112210.0655-10.548-15.5086
111.174-1.267-0.52991.3930.58240.4126-0.9646-0.5987-0.82611.12471.00460.77910.91380.3248-0.042.513-0.1714-0.20841.8932-0.37392.6939-7.3307-45.3745-31.8972
120.00030.0012-0.00160.0178-0.01160.01370.02030.0025-0.01040.0495-0.0913-0.1774-0.13230.07030.07091.90010.01190.01521.97360.07962.4828-20.4859-63.1878-43.3442
134.45932.48940.804417.87391.0640.17420.0619-0.00960.523-0.2709-0.1521.42730.0248-0.05930.09011.2929-0.35550.26580.6693-0.07210.9477-13.2329-50.8226-12.8212
141.8090.0488-0.36442.21321.70173.8132-0.2533-0.3483-0.23210.56720.09490.15011.09390.42730.15840.40340.12070.07610.26960.04660.10589.5869-6.631316.8028
150.1866-0.8921-0.27244.5841.44140.50370.0519-0.05730.18180.10480.3847-1.4980.29840.1576-0.43661.6665-0.2553-0.08961.0154-0.1161.5811-5.8151-56.3816-10.151
161.81374.47761.523522.52896.6944.7152-0.0107-0.142-0.24990.2006-0.40320.93810.5974-0.50780.41390.1487-0.00510.08170.223-0.01210.26464.0823-13.5834-5.3976
170.63024.18190.697334.78768.23192.7653-0.0039-0.0494-0.1966-0.14620.1663-0.67680.07310.3406-0.16241.0564-0.20630.09190.6203-0.08840.9088-4.4233-52.8137-18.9181
181.52043.9743-0.613611.9911-1.23350.3405-0.28810.4847-0.3138-0.92390.1502-0.30360.0174-0.46940.13791.491-0.0974-0.04481.023-0.11481.3062-10.449-76.461-22.6277
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 32
2X-RAY DIFFRACTION2A33 - 320
3X-RAY DIFFRACTION3B10 - 64
4X-RAY DIFFRACTION4B65 - 95
5X-RAY DIFFRACTION5B96 - 125
6X-RAY DIFFRACTION6B126 - 157
7X-RAY DIFFRACTION7C1 - 32
8X-RAY DIFFRACTION8C33 - 320
9X-RAY DIFFRACTION9D10 - 64
10X-RAY DIFFRACTION10D65 - 95
11X-RAY DIFFRACTION11D96 - 125
12X-RAY DIFFRACTION12D126 - 157
13X-RAY DIFFRACTION13E1 - 32
14X-RAY DIFFRACTION14E33 - 320
15X-RAY DIFFRACTION15F10 - 64
16X-RAY DIFFRACTION16F65 - 95
17X-RAY DIFFRACTION17F96 - 125
18X-RAY DIFFRACTION18F126 - 157

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