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- PDB-5ugy: Influenza hemagglutinin in complex with a neutralizing antibody -

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Basic information

Entry
Database: PDB / ID: 5ugy
TitleInfluenza hemagglutinin in complex with a neutralizing antibody
Components
  • (Hemagglutinin ...) x 2
  • CH65 heavy chain
  • CH65 light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / influenza hemagglutinin / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


immunoglobulin complex / immunoglobulin mediated immune response / viral budding from plasma membrane / antigen binding / clathrin-dependent endocytosis of virus by host cell / blood microparticle / host cell surface receptor binding / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane ...immunoglobulin complex / immunoglobulin mediated immune response / viral budding from plasma membrane / antigen binding / clathrin-dependent endocytosis of virus by host cell / blood microparticle / 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 / extracellular region / 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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ribbon / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin / Hemagglutinin / IGL@ protein / IgG H chain
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.801 Å
AuthorsWhittle, J.R.R. / Jenni, S. / Harrison, S.C.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2011
Title: Broadly neutralizing human antibody that recognizes the receptor-binding pocket of influenza virus hemagglutinin.
Authors: Whittle, J.R. / Zhang, R. / Khurana, S. / King, L.R. / Manischewitz, J. / Golding, H. / Dormitzer, P.R. / Haynes, B.F. / Walter, E.B. / Moody, M.A. / Kepler, T.B. / Liao, H.X. / Harrison, S.C.
History
DepositionJan 10, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionJan 25, 2017ID: 3SM5
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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 / struct_asym / struct_conn / 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 / _struct_conn.pdbx_dist_value / _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.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_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 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

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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
H: CH65 heavy chain
I: CH65 heavy chain
J: CH65 heavy chain
L: CH65 light chain
M: CH65 light chain
N: CH65 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)313,20927
Polymers307,57612
Non-polymers5,63315
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area52610 Å2
ΔGint-164 kcal/mol
Surface area119270 Å2
Unit cell
Length a, b, c (Å)154.824, 192.190, 333.219
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain N
21chain L
31chain M
12chain A
22chain C
32chain E
13chain B
23chain D
33chain F
14chain J
24chain H
34chain I

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain NN2 - 211
211chain LL2 - 211
311chain MM2 - 211
112chain AA4 - 8290
212chain CC4 - 8290
312chain EE4 - 8290
113chain BB501 - 673
213chain DD501 - 673
313chain FF501 - 673
114chain JJ1 - 227
214chain HH1 - 227
314chain II1 - 227

NCS ensembles :
ID
1
2
3
4

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Components

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Hemagglutinin ... , 2 types, 6 molecules ACEBDF

#1: Protein Hemagglutinin HA1


Mass: 36024.344 Da / Num. of mol.: 3 / Fragment: UNP residues 18-339
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Solomon Islands/3/2006(H1N1))
Strain: A/Solomon Islands/3/2006(H1N1) / Gene: HA / Plasmid: pFastBac / Cell line (production host): HI-5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A7UPX0, UniProt: A7Y8A6*PLUS
#2: Protein Hemagglutinin HA2


Mass: 19841.041 Da / Num. of mol.: 3 / Fragment: UNP residues 344-516
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Solomon Islands/3/2006(H1N1))
Strain: A/Solomon Islands/3/2006(H1N1) / Gene: HA / Plasmid: pFastBac / Cell line (production host): HI-5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A7UPX0, UniProt: A7Y8I1*PLUS

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Antibody , 2 types, 6 molecules HIJLMN

#3: Antibody CH65 heavy chain


Mass: 24387.211 Da / Num. of mol.: 3 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: S6C4S0
#4: Antibody CH65 light chain


Mass: 22272.625 Da / Num. of mol.: 3 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGL@ / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q8N355

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Sugars , 3 types, 15 molecules

#5: 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.: 6
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
#6: 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.: 3
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
#7: 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.: 6
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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.05 Å3/Da / Density % sol: 69.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.2 M ammonium sulfate, 100 mM Tris, 5% PEG400, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 18, 2011
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.8→29.923 Å / Num. obs: 114569 / % possible obs: 94 % / Observed criterion σ(I): -3 / Redundancy: 5.702 % / Biso Wilson estimate: 40 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.145 / Rrim(I) all: 0.159 / Χ2: 0.997 / Net I/σ(I): 11.09 / Num. measured all: 653278 / Scaling rejects: 2338
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.8-2.873.8215.5760.3163560.1316.40970.9
2.87-2.954.343.1430.565940.2133.55776.2
2.95-3.044.6572.3760.7169190.2972.66981.5
3.04-3.134.9441.7241.0373690.4731.92289.5
3.13-3.235.3711.051.7479070.6711.16398.7
3.23-3.356.0610.7232.7477370.8280.79299.8
3.35-3.476.2940.4854.174390.9250.5399.9
3.47-3.616.3010.3455.8271710.9560.376100
3.61-3.786.2670.2557.7569270.9730.27899.9
3.78-3.966.2660.29.5765870.9860.21899.9
3.96-4.176.2390.14213.1863150.9910.155100
4.17-4.436.2260.10616.7659330.9950.11599.9
4.43-4.736.2050.08220.7856080.9970.0999.9
4.73-5.116.2090.07622.2652320.9970.08399.9
5.11-5.66.1730.07123.2248570.9970.07799.9
5.6-6.266.1260.0723.3243650.9970.077100
6.26-7.236.0110.06226.3638730.9970.06899.8
7.23-8.855.7990.04333.9633160.9980.04799.8
8.85-12.525.7760.0345.6225950.9990.03399.8
12.52-29.9235.3320.02844.9114690.9990.03196.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1RVZ

1rvz


Resolution: 2.801→29.923 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.74
RfactorNum. reflection% reflection
Rfree0.2888 2752 2.47 %
Rwork0.2591 --
obs0.2598 111548 91.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 176.94 Å2 / Biso mean: 49.1023 Å2 / Biso min: 3.52 Å2
Refinement stepCycle: final / Resolution: 2.801→29.923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21513 0 723 0 22236
Biso mean--102.57 --
Num. residues----2781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00322467
X-RAY DIFFRACTIONf_angle_d0.68530618
X-RAY DIFFRACTIONf_chiral_restr0.0473402
X-RAY DIFFRACTIONf_plane_restr0.0073936
X-RAY DIFFRACTIONf_dihedral_angle_d7.20917982
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11N3612X-RAY DIFFRACTION2.508TORSIONAL
12L3612X-RAY DIFFRACTION2.508TORSIONAL
13M3612X-RAY DIFFRACTION2.508TORSIONAL
21A6161X-RAY DIFFRACTION2.508TORSIONAL
22C6161X-RAY DIFFRACTION2.508TORSIONAL
23E6161X-RAY DIFFRACTION2.508TORSIONAL
31B3268X-RAY DIFFRACTION2.508TORSIONAL
32D3268X-RAY DIFFRACTION2.508TORSIONAL
33F3268X-RAY DIFFRACTION2.508TORSIONAL
41J3903X-RAY DIFFRACTION2.508TORSIONAL
42H3903X-RAY DIFFRACTION2.508TORSIONAL
43I3903X-RAY DIFFRACTION2.508TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8006-2.84890.4203630.39852274233739
2.8489-2.90060.3969940.38573788388264
2.9006-2.95640.3981000.38874366446674
2.9564-3.01660.38081350.37944635477079
3.0166-3.08220.40981150.38735033514885
3.0822-3.15380.44371380.35635493563193
3.1538-3.23260.41491450.345869601499
3.2326-3.31990.35741670.321658636030100
3.3199-3.41740.36421370.312858726009100
3.4174-3.52760.32751530.285959386091100
3.5276-3.65340.28311580.260358776035100
3.6534-3.79940.27161460.242659156061100
3.7994-3.9720.28141380.233159546092100
3.972-4.18090.23751180.218959616079100
4.1809-4.4420.25051440.206559246068100
4.442-4.78370.21121440.191559506094100
4.7837-5.26280.22471610.188759556116100
5.2628-6.01890.2361570.21659956152100
6.0189-7.56290.26681630.233960196182100
7.5629-29.92490.22231760.22796115629199

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