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- PDB-4hlz: Crystal Structure of Fab C179 in Complex with a H2N2 influenza vi... -

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Basic information

Entry
Database: PDB / ID: 4hlz
TitleCrystal Structure of Fab C179 in Complex with a H2N2 influenza virus hemagglutinin
Components
  • (Hemagglutinin ...) x 2
  • Fab C179 heavy chain
  • Fab C179 light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / neutralizing antibodies / antibody affinity / antigens / epitopes / glycosylation / hemagglutinin glycoproteins / immunoglobulin Fab fragments / H2N2 subtype / influenza vaccines / avian flu / envelope protein / 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 / 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; 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
Biological speciesInfluenza A virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsDreyfus, C. / Wilson, I.A.
CitationJournal: J.Virol. / Year: 2013
Title: Structure of a classical broadly neutralizing stem antibody in complex with a pandemic h2 influenza virus hemagglutinin.
Authors: Dreyfus, C. / Ekiert, D.C. / Wilson, I.A.
History
DepositionOct 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 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 2.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
B: Hemagglutinin HA2
C: Hemagglutinin HA1
D: Hemagglutinin HA2
E: Hemagglutinin HA1
F: Hemagglutinin HA2
G: Fab C179 heavy chain
H: Fab C179 light chain
I: Fab C179 heavy chain
J: Fab C179 light chain
K: Fab C179 heavy chain
L: Fab C179 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)319,54330
Polymers314,93212
Non-polymers4,61118
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area49930 Å2
ΔGint-346 kcal/mol
Surface area118190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.580, 150.780, 217.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Hemagglutinin ... , 2 types, 6 molecules ACEBDF

#1: Protein Hemagglutinin HA1


Mass: 36504.227 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Japan/305/1957 H2N2 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: C7S226
#2: Protein Hemagglutinin HA2


Mass: 20139.295 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Japan/305/1957 H2N2 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: C7S226

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Antibody , 2 types, 6 molecules GIKHJL

#3: Antibody Fab C179 heavy chain


Mass: 24853.799 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Trichoplusia ni (cabbage looper)
#4: Antibody Fab C179 light chain


Mass: 23479.924 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Trichoplusia ni (cabbage looper)

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Sugars , 4 types, 10 molecules

#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-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
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#7: 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.: 2
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
#8: 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.: 5
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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Non-polymers , 2 types, 8 molecules

#9: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#10: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2

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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: 3.56 Å3/Da / Density % sol: 65.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2 M ammonium sulfate, 0.1 M Tris-HCl pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.03317 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 22, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 100115 / Num. obs: 100115 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.9→2.97 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→39.552 Å / SU ML: 1.19 / σ(F): 1.33 / Phase error: 33.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.284 4964 4.99 %RANDOM
Rwork0.2277 ---
obs0.2305 99399 99.34 %-
all-104363 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.834 Å2 / ksol: 0.316 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.5735 Å20 Å20 Å2
2--1.8366 Å2-0 Å2
3---6.2406 Å2
Refinement stepCycle: LAST / Resolution: 2.9→39.552 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21473 0 293 0 21766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00922366
X-RAY DIFFRACTIONf_angle_d1.35430344
X-RAY DIFFRACTIONf_dihedral_angle_d20.9728197
X-RAY DIFFRACTIONf_chiral_restr0.0863352
X-RAY DIFFRACTIONf_plane_restr0.0063866
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.93290.46441460.41642874X-RAY DIFFRACTION93
2.9329-2.96740.51251690.43752972X-RAY DIFFRACTION95
2.9674-3.00360.44821680.41793062X-RAY DIFFRACTION98
3.0036-3.04160.45011580.41093134X-RAY DIFFRACTION99
3.0416-3.08160.47641560.38793084X-RAY DIFFRACTION99
3.0816-3.12380.38691510.3823141X-RAY DIFFRACTION100
3.1238-3.16840.45391690.35693116X-RAY DIFFRACTION100
3.1684-3.21570.38071860.343094X-RAY DIFFRACTION100
3.2157-3.26590.36421440.31423152X-RAY DIFFRACTION100
3.2659-3.31950.42661560.30613136X-RAY DIFFRACTION100
3.3195-3.37670.37641760.2963114X-RAY DIFFRACTION100
3.3767-3.4380.33251760.28473158X-RAY DIFFRACTION100
3.438-3.50410.33311590.26443171X-RAY DIFFRACTION100
3.5041-3.57560.31621580.26143108X-RAY DIFFRACTION100
3.5756-3.65330.3431720.25593110X-RAY DIFFRACTION100
3.6533-3.73820.32331540.24043188X-RAY DIFFRACTION100
3.7382-3.83160.27421430.2253186X-RAY DIFFRACTION100
3.8316-3.93510.24361660.21273142X-RAY DIFFRACTION100
3.9351-4.05080.26541600.19573183X-RAY DIFFRACTION100
4.0508-4.18140.23421690.17813167X-RAY DIFFRACTION100
4.1814-4.33070.21441560.15773171X-RAY DIFFRACTION100
4.3307-4.50390.18671730.14833155X-RAY DIFFRACTION100
4.5039-4.70850.23541750.15843191X-RAY DIFFRACTION100
4.7085-4.95630.23111660.16683172X-RAY DIFFRACTION100
4.9563-5.26620.26041650.17923181X-RAY DIFFRACTION100
5.2662-5.67170.271510.21163220X-RAY DIFFRACTION100
5.6717-6.24050.25571860.21913210X-RAY DIFFRACTION100
6.2405-7.13890.25381960.22373205X-RAY DIFFRACTION100
7.1389-8.97690.27811710.19683252X-RAY DIFFRACTION100
8.9769-39.55560.25911890.22883386X-RAY DIFFRACTION100

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