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- PDB-4we6: The crystal structure of hemagglutinin HA1 domain from influenza ... -

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Basic information

Entry
Database: PDB / ID: 4we6
TitleThe crystal structure of hemagglutinin HA1 domain from influenza virus A/Perth/142/2007(H3N2)
ComponentsHemagglutinin HA1 chain
KeywordsVIRAL PROTEIN / hemagglutinin / HA1 / H3N2 / influenza virus
Function / homology
Function and homology information


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
Similarity search - Function
Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / 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 ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / 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 / Resolution: 1.904 Å
AuthorsYang, H. / Carney, P.J. / Chang, J.C. / Guo, Z. / Villanueva, J.M. / Stevens, J.
CitationJournal: Virology / Year: 2015
Title: Structure and receptor binding preferences of recombinant human A(H3N2) virus hemagglutinins.
Authors: Yang, H. / Carney, P.J. / Chang, J.C. / Guo, Z. / Villanueva, J.M. / Stevens, J.
History
DepositionSep 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: citation / diffrn_detector ...citation / diffrn_detector / entity / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _diffrn_detector.detector ..._citation.journal_id_CSD / _diffrn_detector.detector / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / refine_hist / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 HA1 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,61710
Polymers62,3642
Non-polymers1,2538
Water10,449580
1
A: Hemagglutinin HA1 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8095
Polymers31,1821
Non-polymers6274
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hemagglutinin HA1 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8095
Polymers31,1821
Non-polymers6274
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.472, 50.567, 182.256
Angle α, β, γ (deg.)90.00, 90.08, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein Hemagglutinin HA1 chain


Mass: 31182.072 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Perth/142/2007(H3N2) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: G8HJ45, UniProt: B2VNP1*PLUS
#2: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / 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
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 580 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 60.81 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 8.5 / Details: 0.1M MgCl2, 0.1 Tris-HCl, pH8.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 56707 / Num. obs: 56707 / % possible obs: 98.2 % / Redundancy: 3.4 % / Net I/σ(I): 12.8

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementResolution: 1.904→44.216 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2011 3023 5.06 %
Rwork0.1695 --
obs0.1711 56707 97.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.904→44.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4294 0 80 580 4954
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.024486
X-RAY DIFFRACTIONf_angle_d1.6836074
X-RAY DIFFRACTIONf_dihedral_angle_d12.811656
X-RAY DIFFRACTIONf_chiral_restr0.135662
X-RAY DIFFRACTIONf_plane_restr0.009784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9041-1.93380.30581290.26352482X-RAY DIFFRACTION93
1.9338-1.96560.27961410.22632513X-RAY DIFFRACTION99
1.9656-1.99940.22891440.20952624X-RAY DIFFRACTION99
1.9994-2.03580.23961400.18832604X-RAY DIFFRACTION99
2.0358-2.0750.23741410.17962581X-RAY DIFFRACTION100
2.075-2.11730.21861420.18252669X-RAY DIFFRACTION100
2.1173-2.16330.20231360.1742526X-RAY DIFFRACTION99
2.1633-2.21370.18691400.16042646X-RAY DIFFRACTION100
2.2137-2.2690.21371400.16762605X-RAY DIFFRACTION100
2.269-2.33040.1931200.16062645X-RAY DIFFRACTION100
2.3304-2.39890.18641400.16682639X-RAY DIFFRACTION100
2.3989-2.47640.21281420.17342590X-RAY DIFFRACTION100
2.4764-2.56490.20151450.16642621X-RAY DIFFRACTION100
2.5649-2.66750.19141470.15742652X-RAY DIFFRACTION99
2.6675-2.78890.20951230.15772569X-RAY DIFFRACTION99
2.7889-2.93590.20621390.16182575X-RAY DIFFRACTION99
2.9359-3.11980.19611340.1642620X-RAY DIFFRACTION98
3.1198-3.36070.20871330.15892571X-RAY DIFFRACTION97
3.3607-3.69870.16481350.15232514X-RAY DIFFRACTION95
3.6987-4.23350.17111480.14892533X-RAY DIFFRACTION95
4.2335-5.33240.18671360.15422385X-RAY DIFFRACTION90
5.3324-44.22770.21691280.20622532X-RAY DIFFRACTION91
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)
10.5957-0.54350.6471.2202-1.22622.44730.0097-0.01770.07560.0277-0.03750.0140.21920.0538-0.0255-0.0205-0.01990.01360.05580.00970.069517.0786-16.785359.6331
21.0016-0.91420.56860.7153-0.1132.2178-0.048-0.16310.07140.35010.00920.0214-0.2403-0.3501-0.01180.1272-0.017-0.0270.0962-0.02970.049617.6122-12.535175.2773
30.3434-0.73530.08441.0686-0.66020.6120.1367-0.05110.0379-0.1765-0.0650.12870.0185-0.19940.00850.0169-0.02240.00720.05880.04640.0977.4286-9.305246.3813
40.69350.6281-0.69251.5865-1.21832.59070.04320.0082-0.0425-0.0456-0.05950.0275-0.36780.0665-0.0166-0.11590.0394-0.01040.02470.01130.0643-4.1285-31.347931.4802
50.69520.7484-0.5750.67250.00722.2417-0.03720.1376-0.0703-0.3663-0.009-0.00290.1963-0.3252-0.03420.0970.00960.01110.1085-0.010.0673-3.5471-35.587215.8347
60.21940.5654-0.05960.9222-0.56680.80060.14040.0315-0.03370.1688-0.05620.1439-0.057-0.17950.00040.04690.01640.00140.07760.04650.1122-13.7939-38.843244.7235
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 135 )
2X-RAY DIFFRACTION2chain 'A' and (resid 136 through 207 )
3X-RAY DIFFRACTION3chain 'A' and (resid 208 through 270 )
4X-RAY DIFFRACTION4chain 'B' and (resid -2 through 135 )
5X-RAY DIFFRACTION5chain 'B' and (resid 136 through 207 )
6X-RAY DIFFRACTION6chain 'B' and (resid 208 through 270 )

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