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- PDB-1ru7: 1934 Human H1 Hemagglutinin -

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Basic information

Entry
Database: PDB / ID: 1ru7
Title1934 Human H1 Hemagglutinin
Components(hemagglutinin) x 2
KeywordsVIRAL PROTEIN / HEMAGGLUTININ / ENVELOPE PROTEIN / GLYCOPROTEIN
Function / homology
Function and homology information


Transport of HA trimer, NA tetramer and M2 tetramer from the endoplasmic reticulum to the Golgi Apparatus / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral mRNA Translation ...Transport of HA trimer, NA tetramer and M2 tetramer from the endoplasmic reticulum to the Golgi Apparatus / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral mRNA Translation / viral budding from plasma membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / 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 / extracellular region / membrane / plasma 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
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSkehel, J.J. / Gamblin, S.J. / Haire, L.F. / Russell, R.J. / Stevens, D.J. / Xiao, B. / Ha, Y. / Vasisht, N. / Steinhauer, D.A. / Daniels, R.S.
CitationJournal: Science / Year: 2004
Title: The structure and receptor binding properties of the 1918 influenza hemagglutinin.
Authors: Gamblin, S.J. / Haire, L.F. / Russell, R.J. / Stevens, D.J. / Xiao, B. / Ha, Y. / Vasisht, N. / Steinhauer, D.A. / Daniels, R.S. / Elliot, A. / Wiley, D.C. / Skehel, J.J.
History
DepositionDec 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 2, 2013Group: Other
Revision 1.4Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE The sequence of this protein is not available in any reference sequence database. Residue ...SEQUENCE The sequence of this protein is not available in any reference sequence database. Residue (B ASN 42 ) and residue (B GLY 43 ) are not linked, distance of C-N bond is 2.60. Residue (J ASN 42 ) and residue (J GLY 43 ) are not linked, distance of C-N bond is 2.63.

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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
J: hemagglutinin
K: hemagglutinin
L: hemagglutinin


Theoretical massNumber of molelcules
Total (without water)329,94412
Polymers329,94412
Non-polymers00
Water23,3111294
1
A: hemagglutinin
B: hemagglutinin
C: hemagglutinin
D: hemagglutinin
E: hemagglutinin
F: hemagglutinin


Theoretical massNumber of molelcules
Total (without water)164,9726
Polymers164,9726
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28290 Å2
ΔGint-154 kcal/mol
Surface area58330 Å2
MethodPISA
2
G: hemagglutinin
H: hemagglutinin
I: hemagglutinin
J: hemagglutinin
K: hemagglutinin
L: hemagglutinin


Theoretical massNumber of molelcules
Total (without water)164,9726
Polymers164,9726
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28310 Å2
ΔGint-154 kcal/mol
Surface area58310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)227.515, 131.084, 174.383
Angle α, β, γ (deg.)90.00, 109.81, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
hemagglutinin


Mass: 36748.371 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: BROMELAIN DIGESTED
Source: (natural) Influenza A virus (A/Puerto Rico/8/34(H1N1))
Genus: Influenzavirus A / Species: Influenza A virus / Strain: A-PUERTO RICO-8-34 / References: UniProt: Q82766, UniProt: P03452*PLUS
#2: Protein
hemagglutinin


Mass: 18242.221 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: Hemagglutinin HA2 chain
Source: (natural) Influenza A virus (A/Puerto Rico/8/34(H1N1))
Genus: Influenzavirus A / Species: Influenza A virus / Strain: A-PUERTO RICO-8-34 / References: UniProt: Q82766, UniProt: P03452*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1294 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.71 Å3/Da / Density % sol: 66.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 18% PEG3350, TrisHCl, KSCN, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 20, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 213315 / Num. obs: 199084 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 9.7
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 1.8 / % possible all: 47.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JSD

1jsd


Resolution: 2.3→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.266 9873 Random
Rwork0.235 --
all0.235 213315 -
obs0.235 199084 -
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23020 0 0 1294 24314

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