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- PDB-1htm: STRUCTURE OF INFLUENZA HAEMAGGLUTININ AT THE PH OF MEMBRANE FUSION -

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Basic information

Entry
Database: PDB / ID: 1htm
TitleSTRUCTURE OF INFLUENZA HAEMAGGLUTININ AT THE PH OF MEMBRANE FUSION
Components
  • HEMAGGLUTININ HA1 CHAIN
  • HEMAGGLUTININ HA2 CHAIN
KeywordsVIRAL PROTEIN / INFLUENZA VIRUS HEMAGGLUTININ
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 / 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
Biological speciesuncultured beta proteobacterium UMTRA-608 (environmental samples)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsBullough, P.A. / Hughson, F.M. / Skehel, J.J. / Wiley, D.C.
Citation
Journal: Nature / Year: 1994
Title: Structure of influenza haemagglutinin at the pH of membrane fusion.
Authors: Bullough, P.A. / Hughson, F.M. / Skehel, J.J. / Wiley, D.C.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystals of a Fragment of Influenza Haemagglutinin in the Low Ph Induced Conformation
Authors: Bullough, P.A. / Hughson, F.M. / Treharne, A.C. / Ruigrok, R.W.H. / Skehel, J.J. / Wiley, D.C.
#2: Journal: J.Mol.Biol. / Year: 1990
Title: Refinement of the Influenza Virus Hemagglutinin by Simulated Annealing
Authors: Weis, W.I. / Brunger, A.T. / Skehel, J.J. / Wiley, D.C.
#3: Journal: J.Gen.Virol. / Year: 1988
Title: Studies on the Structure of the Influenza Virus Haemagglutinin at the Ph of Membrane Fusion
Authors: Ruigrok, R.W.H. / Aitken, A. / Calder, L.J. / Martin, S.R. / Skehel, J.J. / Wharton, S.A. / Weis, W. / Wiley, D.C.
#4: Journal: J.Gen.Virol. / Year: 1983
Title: Analyses of the Antigenicity of Influenza Haemagglutinin at the Ph Optimum for Virus-Mediated Membrane Fusion
Authors: Daniels, R.S. / Douglas, A.R. / Skehel, J.J.
#5: Journal: Proc.Natl.Acad.Sci.USA / Year: 1982
Title: Changes in the Conformation of Influenza Virus Hemagglutinin at the Ph Optimum of Virus-Mediated Membrane Fusion
Authors: Skehel, J.J. / Bayley, P.M. / Brown, E.B. / Martin, S.R. / Waterfield, M.D. / White, J.M. / Wilson, I.A. / Wiley, D.C.
#6: Journal: Nature / Year: 1981
Title: Structure of the Haemagglutinin Membrane Glycoprotein of Influenza Virus at 3 Angstroms Resolution
Authors: Wilson, I.A. / Skehel, J.J. / Wiley, D.C.
History
DepositionNov 2, 1994Processing site: BNL
Revision 1.0Feb 14, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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


Theoretical massNumber of molelcules
Total (without water)57,1336
Polymers57,1336
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12090 Å2
ΔGint-93 kcal/mol
Surface area18880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.700, 231.700, 53.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.1122, 0.1026, -0.9884), (0.9921, 0.0453, 0.1174), (0.0568, -0.9937, -0.0967)52.9144, 5.412, 73.1627
2given(0.0496, 0.9988, -0.0032), (0.1893, -0.0128, -0.9816), (-0.9809, 0.0476, -0.1896)-12.046, 66.2165, 64.9402
DetailsTBHA2 IS A TRIMER WHOSE IDENTICAL SUBUNITS CONSIST OF RESIDUES 1 - 27 OF THE HA1 CHAIN AND RESIDUES 38 - 175 OF THE HA2 CHAIN. WITHIN EACH SUBUNIT, THE HA1 AND HA2 CHAINS ARE LINKED BY A SINGLE DISULFIDE BOND BETWEEN HA1 RESIDUE 14 AND HA2 RESIDUE 137. AS IN EARLIER HA STRUCTURES (SEE REFERENCES), CHAINS HA1 AND HA2 OF SUBUNIT 1 HAVE BEEN ASSIGNED CHAIN IDENTIFIERS *A* AND *B*, RESPECTIVELY. CHAINS HA1 AND HA2 OF SUBUNIT 2 HAVE BEEN ASSIGNED CHAIN IDENTIFIERS *C* AND *D*, RESPECTIVELY. CHAINS HA1 AND HA2 OF SUBUNIT 3 HAVE BEEN ASSIGNED CHAIN IDENTIFIERS *E* AND *F*, RESPECTIVELY. IN ADDITION, 35 WATER MOLECULES/TRIMER ARE INCLUDED, NUMBERED FROM 1001 WITH NO CHAIN IDENTIFIER. THE TRANSFORMATION PRESENTED ON *MTRIX 1* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS *A* AND *B* WHEN APPLIED TO CHAINS *C* AND *D*. THE TRANSFORMATION PRESENTED ON *MTRIX 2* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS *A* AND *B* WHEN APPLIED TO CHAINS *E* AND *F*. MONOMERS 1 AND 2 SUPERIMPOSE WITH AN RMS DEVIATION BETWEEN ALPHA CARBON ATOMS OF ABOUT 0.8 ANGSTROMS; MONOMERS 1 AND 3 SUPERIMPOSE WITH AN RMS DEVIATION BETWEEN ALPHA CARBON ATOMS OF ABOUT 1.2 ANGSTROMS.

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Components

#1: Protein/peptide HEMAGGLUTININ HA1 CHAIN


Mass: 2776.066 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured beta proteobacterium UMTRA-608 (environmental samples)
References: UniProt: P03437
#2: Protein HEMAGGLUTININ HA2 CHAIN


Mass: 16268.125 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured beta proteobacterium UMTRA-608 (environmental samples)
References: UniProt: P03437
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Compound detailsIN THE VIRUS, HEMAGGLUTININ IS A TRIMER OF IDENTICAL SUBUNITS, EACH CONSISTING OF A DISULFIDE- ...IN THE VIRUS, HEMAGGLUTININ IS A TRIMER OF IDENTICAL SUBUNITS, EACH CONSISTING OF A DISULFIDE-LINKED DIMER OF HA1 AND HA2 CHAINS. THE HA1 CHAIN CONSISTS OF 328 RESIDUES AND THE HA2 CHAIN CONSISTS OF 220 RESIDUES. HEMAGGLUTININ MAY BE SOLUBILIZED FROM THE VIRAL MEMBRANE BY BROMELAIN DIGESTION, WHICH REMOVES THE C-TERMINAL HYDROPHOBIC (ANCHORING) DOMAIN FROM CHAIN HA2. AFTER BROMELAIN DIGESTION CHAIN HA2 CONSISTS OF 175 RESIDUES; THE STRUCTURE OF THIS SOLUBLE TRIMER HAS BEEN DETERMINED PREVIOUSLY (SEE REFERENCES). AFTER EXPOSURE TO THE PH OF MEMBRANE FUSION, THE BROMELAIN-SOLUBILIZED TRIMERS AGGREGATE AND BECOME SUSCEPTIBLE TO DIGESTION WITH TRYPSIN AND THERMOLYSIN. SUCCESSIVE DIGESTION WITH THESE PROTEASES YIELDS A SOLUBLE TRIMER CALLED TBHA2, WHOSE STRUCTURE IS PRESENTED IN THIS ENTRY.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.6 Å3/Da / Density % sol: 73.26 %
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion, hanging drop / Details: Bullough, P.A., (1994) J.Mol.Biol., 236, 1262.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18-15 mg/mlTBHA21drop
210 mMphosphate1drop
3150 mM1dropNaCl
40.01 %sodium azide1drop
51 mMEDTA1drop
60.1 Mcitric acid1drop
755-65 %satammonium sulfate1reservoir
80.1 MADA1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→6 Å / Num. obs: 27793 / % possible obs: 81.05 % / Observed criterion σ(I): 2

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rfree: 0.291 / Rfactor Rwork: 0.222 / Rfactor obs: 0.222 / Highest resolution: 2.5 Å
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3092 0 0 37 3129
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.17
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 6 Å / Num. reflection obs: 25888 / Rfactor obs: 0.222 / Rfactor Rfree: 0.291 / Rfactor Rwork: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.17

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