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- PDB-4cr0: Crystal Structure of H5 (VN1194) Asn186Lys/Gly143Arg Mutant Haema... -

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Basic information

Entry
Database: PDB / ID: 4cr0
TitleCrystal Structure of H5 (VN1194) Asn186Lys/Gly143Arg Mutant Haemagglutinin
Components
  • Hemagglutinin HA1
  • Hemagglutinin HA2
KeywordsVIRAL PROTEIN / SIALIC ACID / GLYCOPROTEIN / VIRUS RECEPTOR / AVIAN FLU / SIALYLLACTOSAMINE / 3SLN / 3'SLN / 6SLN / 6'SLN / LSTA
Function / homology
Function and homology information


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 / 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
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsCollins, P.J. / Vachieri, S.G. / Xiong, X. / Xiao, H. / Martin, S.R. / Coombs, P.J. / Liu, J. / Walker, P.A. / Lin, Y.P. / McCauley, J.W. ...Collins, P.J. / Vachieri, S.G. / Xiong, X. / Xiao, H. / Martin, S.R. / Coombs, P.J. / Liu, J. / Walker, P.A. / Lin, Y.P. / McCauley, J.W. / Gamblin, S.J. / Skehel, J.J.
CitationJournal: Virology / Year: 2014
Title: Enhanced Human Receptor Binding by H5 Haemagglutinins.
Authors: Xiong, X. / Xiao, H. / Martin, S.R. / Coombs, P.J. / Liu, J. / Collins, P.J. / Vachieri, S.G. / Walker, P.A. / Lin, Y.P. / Mccauley, J.W. / Gamblin, S.J. / Skehel, J.J.
History
DepositionFeb 21, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Nov 7, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / entity_src_nat / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_mutation ..._entity.pdbx_description / _entity.pdbx_mutation / _entity.src_method / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / 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
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 20, 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
B: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0396
Polymers56,1542
Non-polymers8854
Water2,342130
1
A: Hemagglutinin HA1
B: Hemagglutinin HA2
hetero molecules

A: Hemagglutinin HA1
B: Hemagglutinin HA2
hetero molecules

A: Hemagglutinin HA1
B: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,11618
Polymers168,4626
Non-polymers2,65412
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area29140 Å2
ΔGint-148.1 kcal/mol
Surface area61620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.950, 77.950, 210.411
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Hemagglutinin HA1


Mass: 37065.984 Da / Num. of mol.: 1
Fragment: HA1 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 17-340
Mutation: N168K,G143R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Gallus gallus (chicken) / References: UniProt: Q6DQ34
#2: Protein Hemagglutinin HA2


Mass: 19087.953 Da / Num. of mol.: 1
Fragment: HA2 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 347-512
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Gallus gallus (chicken) / References: UniProt: Q6DQ34
#3: 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: 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 2.7 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growDetails: 0.1 M MOPS PH 7.0, 12% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.65→67.51 Å / Num. obs: 20820 / % possible obs: 99.1 % / Observed criterion σ(I): 2.6 / Redundancy: 5.5 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.8
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.6 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0046refinement
xia2data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BGW

4bgw


Resolution: 2.65→105.21 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.875 / SU B: 26.777 / SU ML: 0.279 / Cross valid method: THROUGHOUT / ESU R: 0.64 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1071 5.2 %RANDOM
Rwork0.2245 ---
obs0.22651 19715 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.967 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20.52 Å20 Å2
2--1.04 Å20 Å2
3----3.38 Å2
Refinement stepCycle: LAST / Resolution: 2.65→105.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3837 0 56 130 4023
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193990
X-RAY DIFFRACTIONr_bond_other_d0.0020.023675
X-RAY DIFFRACTIONr_angle_refined_deg1.1631.9535410
X-RAY DIFFRACTIONr_angle_other_deg0.7183.0038433
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2495479
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.30325.075199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.49215673
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0841518
X-RAY DIFFRACTIONr_chiral_restr0.0640.2584
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024557
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02937
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_it0.5831.7131922
X-RAY DIFFRACTIONr_mcbond_other0.5831.7131921
X-RAY DIFFRACTIONr_mcangle_it1.0692.5692399
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.841.8252068
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
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 71 -
Rwork0.342 1288 -
obs--87.85 %
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)
10.1233-0.0451-0.76310.03120.36665.29720.07460.05270.0417-0.07680.0487-0.0001-0.65140.1316-0.12320.4556-0.0272-0.00880.47850.01780.238610.548-25.5847-18.4435
22.53420.18360.18631.05880.13992.29060.0121-0.00750.0222-0.06650.00840.0569-0.20630.017-0.02050.1128-0.01430.02090.0198-0.01650.06222.8051-25.339216.7665
30.54280.38622.62030.42681.903612.7867-0.0003-0.11540.0307-0.1022-0.0173-0.0073-0.1021-0.68030.01760.2993-0.07740.02220.71230.02360.190810.5418-26.8833-26.6083
41.44691.3156-1.85241.6456-2.99976.65280.1083-0.20040.04170.1747-0.0451-0.0276-0.45320.0417-0.06320.2163-0.0255-0.01060.2643-0.02320.1865.0649-28.7014-58.3361
51.9295-3.08274.17476.8035-4.332412.5031-0.01210.40650.4156-0.4894-0.5327-0.6091-0.48140.90050.54480.2421-0.0834-0.0980.38110.20240.42165.6669-40.8428-10.3876
60.5580.1135-0.7990.7007-2.899313.87320.1231-0.1499-0.15010.013-0.1699-0.06810.05880.43610.04680.2085-0.0846-0.0550.21750.02670.19323.7727-37.3764-56.5328
710.15661.2568-3.95083.1082.06944.98210.26230.07950.20790.1485-0.0702-0.1296-0.2907-0.2753-0.19210.2510.0299-0.03320.22030.05770.1469-1.2812-22.6375-77.7572
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 105
2X-RAY DIFFRACTION2A106 - 262
3X-RAY DIFFRACTION3A263 - 321
4X-RAY DIFFRACTION4B1 - 60
5X-RAY DIFFRACTION5B61 - 84
6X-RAY DIFFRACTION6B85 - 141
7X-RAY DIFFRACTION7B142 - 161

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