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- PDB-4mhh: Crystal structure of Fab H5M9 in complex with influenza virus hem... -

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Basic information

Entry
Database: PDB / ID: 4mhh
TitleCrystal structure of Fab H5M9 in complex with influenza virus hemagglutinin from A/Viet Nam/1203/2004 (H5N1)
Components
  • (H5M9 antibody, ...) x 2
  • (Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / H5N1 influenza virus / broadly neutralizing murine antibody / escape mutant / passive immunotherapy / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 ...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 / identical protein binding / 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 / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.564 Å
AuthorsZhu, X. / Wilson, I.A.
CitationJournal: J.Virol. / Year: 2013
Title: A Unique and Conserved Neutralization Epitope in H5N1 Influenza Viruses Identified by an Antibody against the A/Goose/Guangdong/1/96 Hemagglutinin.
Authors: Zhu, X. / Guo, Y.H. / Jiang, T. / Wang, Y.D. / Chan, K.H. / Li, X.F. / Yu, W. / McBride, R. / Paulson, J.C. / Yuen, K.Y. / Qin, C.F. / Che, X.Y. / Wilson, I.A.
History
DepositionAug 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 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 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemagglutinin HA1 chain
C: Hemagglutinin HA1 chain
E: Hemagglutinin HA1 chain
L: H5M9 antibody, light chain (kappa)
I: H5M9 antibody, light chain (kappa)
K: H5M9 antibody, light chain (kappa)
B: Hemagglutinin HA2 chain
D: Hemagglutinin HA2 chain
F: Hemagglutinin HA2 chain
H: H5M9 antibody, heavy chain (IgG1)
G: H5M9 antibody, heavy chain (IgG1)
J: H5M9 antibody, heavy chain (IgG1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)330,81333
Polymers320,44312
Non-polymers10,37021
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Hemagglutinin HA1 chain
C: Hemagglutinin HA1 chain
E: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
D: Hemagglutinin HA2 chain
F: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,19324
Polymers176,4876
Non-polymers9,70618
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37100 Å2
ΔGint-9 kcal/mol
Surface area68980 Å2
MethodPISA
3
L: H5M9 antibody, light chain (kappa)
H: H5M9 antibody, heavy chain (IgG1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2063
Polymers47,9852
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-22 kcal/mol
Surface area19470 Å2
MethodPISA
4
I: H5M9 antibody, light chain (kappa)
G: H5M9 antibody, heavy chain (IgG1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2063
Polymers47,9852
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-18 kcal/mol
Surface area19450 Å2
MethodPISA
5
K: H5M9 antibody, light chain (kappa)
J: H5M9 antibody, heavy chain (IgG1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2063
Polymers47,9852
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-21 kcal/mol
Surface area19740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.007, 251.423, 230.811
Angle α, β, γ (deg.)90.00, 107.01, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Hemagglutinin ... , 2 types, 6 molecules ACEBDF

#1: Protein Hemagglutinin HA1 chain


Mass: 37948.020 Da / Num. of mol.: 3 / Fragment: receptor binding domain (UNP residues 17-346)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/viet nam/1203/2004 / Gene: HA / Plasmid: pfastbac-HT / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q6DQ33, UniProt: Q9Q0U6*PLUS
#3: Protein Hemagglutinin HA2 chain


Mass: 20881.104 Da / Num. of mol.: 3 / Fragment: membrane fusion domain (UNP residues 347-520)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/viet nam/1203/2004 / Gene: HA / Plasmid: pfastbac-HT / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q6DQ33, UniProt: Q6J8F6*PLUS

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Antibody , 2 types, 6 molecules LIKHGJ

#2: Antibody H5M9 antibody, light chain (kappa)


Mass: 24049.486 Da / Num. of mol.: 3 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
#4: Antibody H5M9 antibody, heavy chain (IgG1)


Mass: 23935.797 Da / Num. of mol.: 3 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)

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Sugars , 5 types, 21 molecules

#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#8: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#9: 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

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Details

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: 6.15 Å3/Da / Density % sol: 80 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 2% PEG4000, 2.2 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 1, 2009
RadiationMonochromator: double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.564→50 Å / Num. obs: 85101 / % possible obs: 94.9 % / Observed criterion σ(I): -3
Reflection shellResolution: 3.564→3.83 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.2 / Rsym value: 0.94 / % possible all: 84.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3GBM, 2VL5, AND 1P7K

3gbm

2vl5

1p7k


Resolution: 3.564→47.3 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.238 4209 5 %RANDOM
Rwork0.2012 ---
obs0.203 84244 91.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.564→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22098 0 686 0 22784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01223382
X-RAY DIFFRACTIONf_angle_d1.55731757
X-RAY DIFFRACTIONf_dihedral_angle_d21.1028641
X-RAY DIFFRACTIONf_chiral_restr0.0723572
X-RAY DIFFRACTIONf_plane_restr0.014034
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.564-3.60470.5025290.4488578X-RAY DIFFRACTION20
3.6047-3.64710.50571090.47821860X-RAY DIFFRACTION64
3.6471-3.69160.44971450.38792268X-RAY DIFFRACTION79
3.6916-3.73830.43941280.44962304X-RAY DIFFRACTION80
3.7383-3.78740.36531280.35342568X-RAY DIFFRACTION88
3.7874-3.83930.42491400.36452598X-RAY DIFFRACTION89
3.8393-3.89410.43361370.36132563X-RAY DIFFRACTION89
3.8941-3.95220.3911340.33732676X-RAY DIFFRACTION91
3.9522-4.0140.33381430.27262782X-RAY DIFFRACTION95
4.014-4.07970.29611530.27022758X-RAY DIFFRACTION96
4.0797-4.150.29781140.25982852X-RAY DIFFRACTION97
4.15-4.22550.28091580.25692851X-RAY DIFFRACTION98
4.2255-4.30670.26091420.22612858X-RAY DIFFRACTION98
4.3067-4.39450.25251520.21052855X-RAY DIFFRACTION98
4.3945-4.490.21551280.19772884X-RAY DIFFRACTION98
4.49-4.59440.24221290.18562853X-RAY DIFFRACTION98
4.5944-4.70920.21171430.18662885X-RAY DIFFRACTION98
4.7092-4.83640.22831670.17942843X-RAY DIFFRACTION98
4.8364-4.97850.20811340.17542898X-RAY DIFFRACTION98
4.9785-5.1390.22781620.17362832X-RAY DIFFRACTION98
5.139-5.32250.21411730.16282834X-RAY DIFFRACTION98
5.3225-5.53530.19051560.16532865X-RAY DIFFRACTION98
5.5353-5.78680.20161440.16792856X-RAY DIFFRACTION98
5.7868-6.09130.2041560.17542857X-RAY DIFFRACTION98
6.0913-6.4720.21641480.17332864X-RAY DIFFRACTION98
6.472-6.97030.21211430.18392828X-RAY DIFFRACTION97
6.9703-7.66910.23971610.18312854X-RAY DIFFRACTION97
7.6691-8.77270.19611500.1582832X-RAY DIFFRACTION97
8.7727-11.02950.18461440.14162858X-RAY DIFFRACTION97
11.0295-47.30420.20821590.19052821X-RAY DIFFRACTION95

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