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- PDB-6ml8: Crystal structure of hemagglutinin from H1N1 Influenza A virus A/... -

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Basic information

Entry
Database: PDB / ID: 6ml8
TitleCrystal structure of hemagglutinin from H1N1 Influenza A virus A/Denver/57 bound to the C05 antibody
Components
  • (C05 antibody Fab ...) x 2
  • (Hemagglutinin) x 2
KeywordsVIRAL PROTEIN / NIAID / structural genomics / influenza virus / vaccine development / broadly neutralizing antibody / strain-specific neutralization / influenzavirus / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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
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
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.92 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Sci Rep / Year: 2023
Title: Structural characterisation of hemagglutinin from seven Influenza A H1N1 strains reveal diversity in the C05 antibody recognition site.
Authors: Ghafoori, S.M. / Petersen, G.F. / Conrady, D.G. / Calhoun, B.M. / Stigliano, M.Z.Z. / Baydo, R.O. / Grice, R. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E. / Forwood, J.K.
History
DepositionSep 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: 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.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 24, 2023Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
H: C05 antibody Fab heavy chain
L: C05 antibody Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,3967
Polymers105,6374
Non-polymers1,7603
Water81145
1
A: Hemagglutinin
B: Hemagglutinin
H: C05 antibody Fab heavy chain
L: C05 antibody Fab light chain
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
H: C05 antibody Fab heavy chain
L: C05 antibody Fab light chain
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
H: C05 antibody Fab heavy chain
L: C05 antibody Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)322,18921
Polymers316,91012
Non-polymers5,2799
Water21612
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
Unit cell
Length a, b, c (Å)118.460, 118.460, 162.440
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Hemagglutinin


Mass: 37002.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Denver/1957(H1N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q2IBI1
#2: Protein Hemagglutinin


Mass: 18946.006 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Denver/1957(H1N1))
Strain: A/Denver/1957(H1N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q2IBI1

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Antibody , 2 types, 2 molecules HL

#3: Antibody C05 antibody Fab heavy chain


Mass: 26321.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#4: Antibody C05 antibody Fab light chain


Mass: 23367.018 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)

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Sugars , 3 types, 3 molecules

#5: 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
#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.: 1
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: 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.: 1
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

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Non-polymers , 1 types, 45 molecules

#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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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: 3.1 Å3/Da / Density % sol: 60.34 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: InvbJ.18715.a.KN11/HosaA.20194.a.TC11 batch PD39296/PD38299 at a combined complex 10 mg/mL against PACT screen condition G9: 0.2 M potassium/sodium tartrate, 0.1 M BisTris Propane pH 7.5, ...Details: InvbJ.18715.a.KN11/HosaA.20194.a.TC11 batch PD39296/PD38299 at a combined complex 10 mg/mL against PACT screen condition G9: 0.2 M potassium/sodium tartrate, 0.1 M BisTris Propane pH 7.5, 20% PEG 3350 supplemented with 20% ethylene glycol as cryo-protectant, crystal tracking ID 300847g9, unique puck ID sto6-4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.92→47.886 Å / Num. obs: 29212 / % possible obs: 99.9 % / Redundancy: 7.324 % / Biso Wilson estimate: 66.752 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.116 / Χ2: 1.032 / Net I/σ(I): 15.23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.92-37.5560.977221170.7261.05100
3-3.087.540.782.5220760.7970.838100
3.08-3.177.5430.5773.4420100.8870.62100
3.17-3.267.5270.4664.3119900.9250.501100
3.26-3.377.5130.3655.4519010.9480.393100
3.37-3.497.4160.2827.2618500.9780.30399.9
3.49-3.627.4870.2029.8317680.9830.217100
3.62-3.777.3020.18211.2217200.9860.196100
3.77-3.947.2730.14313.8516620.9920.15499.9
3.94-4.137.3740.11216.8415570.9940.12100
4.13-4.357.3080.08920.2215270.9970.096100
4.35-4.627.1920.0725.2114190.9970.076100
4.62-4.947.1790.06526.7213650.9980.07100
4.94-5.337.1950.06127.3112550.9980.066100
5.33-5.847.1760.05828.2411630.9980.063100
5.84-6.537.1790.05628.9910780.9980.061100
6.53-7.547.0670.04633.019260.9990.04999.9
7.54-9.236.8720.03339.978130.9990.035100
9.23-13.066.5830.02545.8564710.02799.7
13.06-47.8865.7340.02443.863680.9990.02694.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIX1.14_3219refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EDB, 4FNL

4edb

4fnl


Resolution: 2.92→47.886 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.21
RfactorNum. reflection% reflection
Rfree0.2642 1534 5.25 %
Rwork0.2012 --
obs0.2045 29208 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 249.63 Å2 / Biso mean: 87.0651 Å2 / Biso min: 23.4 Å2
Refinement stepCycle: final / Resolution: 2.92→47.886 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6796 0 117 45 6958
Biso mean--115.67 52.68 -
Num. residues----917
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.9202-3.01440.39691310.328725022633
3.0144-3.12220.33591590.270124382597
3.1222-3.24710.32741230.239324792602
3.2471-3.39490.26341140.224325352649
3.3949-3.57380.30861200.222624832603
3.5738-3.79770.25581530.208925032656
3.7977-4.09070.27461260.189924972623
4.0907-4.50210.2421490.16125012650
4.5021-5.15290.20971670.154825202687
5.1529-6.48960.2461480.190525472695
6.4896-47.89250.27071440.20926692813
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)
10.73050.09180.2371.0907-0.63925.1867-0.0969-0.36280.33940.9376-0.05610.005-0.7875-0.03050.08430.9820.0240.00140.5586-0.19070.51310.597-45.803550.3448
22.5958-0.2696-0.41210.9908-0.08374.8733-0.08790.07410.2788-0.12410.0221-0.1929-0.35970.23980.08360.3779-0.0711-0.05640.1757-0.04550.43997.5671-44.475115.7643
34.5656-0.96894.50592.1798-1.62467.68770.07360.1551-0.2903-0.28090.0639-0.02190.10280.2596-0.14570.28860.01270.05290.1974-0.02940.47448.0839-54.89811.1619
40.9823-0.0927-0.61571.2658-0.88384.02410.0208-0.33320.09340.4519-0.0271-0.0269-0.58760.0390.03570.4711-0.0265-0.06160.3535-0.08440.48122.5083-50.731238.3062
50.7746-0.41590.270.47010.23160.6237-0.552-0.76380.26730.50990.75650.0746-1.04210.47130.12112.1584-0.02920.10321.8703-0.24720.6317-0.4088-48.88397.311
61.7696-0.55090.3961.8011.19361.1581-0.1727-0.92550.7110.88820.142-0.1955-0.83531.0977-0.60471.3216-0.2897-0.04411.2271-0.21970.57768.9197-52.914982.9178
70.5627-0.1427-1.20110.04870.2922.5628-0.2158-0.4725-0.05470.1545-0.36450.01750.15130.60080.76310.8354-0.0673-0.09570.71010.20880.53317.8944-57.756653.599
81.30060.29920.34721.08060.04191.27180.2735-0.9140.08451.13140.18190.0348-0.4558-0.44840.25751.40340.0127-0.00950.9762-0.10160.2756-1.458-60.247575.4637
93.6498-0.6150.64770.4979-0.37260.2887-0.1362-0.06020.63310.8029-0.0739-0.1241-1.4563-0.23770.22172.46580.125-0.52561.7409-0.19930.738712.8846-51.3835107.7566
103.1165-0.80510.73074.3735-1.41536.01520.12490.42610.1396-0.1671-0.07430.367-0.3949-0.3535-0.09810.28650.0394-0.02860.36310.00050.5368-7.249-26.1313-10.9963
116.43262.49191.54661.7231-1.76828.5269-0.04762.2989-0.245-0.63710.37680.2004-0.5168-0.78030.04561.05440.4882-0.26271.7037-0.13490.8286-11.6736-23.4064-41.0167
125.17195.90663.05258.46711.29235.1372-0.8103-0.00080.1324-1.863-0.81372.2483-0.1419-2.35881.61671.16140.0574-0.32981.6056-0.49821.0261-11.7058-33.2633-49.0362
132.51091.12213.19093.6044-1.60857.01590.04450.1886-0.5668-0.49970.33560.30510.8082-0.0337-0.95451.48520.742-0.60862.5271-0.79831.4315-20.3386-25.7757-39.0229
144.871-0.1295-0.45483.36751.11265.24550.22590.27180.1593-0.3535-0.0754-0.3807-0.39911.1715-0.22510.427-0.1181-0.04470.77290.04610.52615.2409-28.3726-19.3779
154.8123-0.8552-1.94363.64671.32954.7917-0.00520.2428-0.03490.02890.088-0.09350.03470.4911-0.05490.3059-0.0304-0.00910.57020.00760.544410.4267-33.36-19.1851
163.31530.11381.20312.968-0.19823.80090.89132.74270.0872-1.654-0.23810.7108-0.2424-0.36470.32070.9770.3079-0.21672.29130.13860.51537.8325-29.4829-44.4505
170.76370.61370.6991.2-0.56772.45660.08580.80670.5511-1.3176-0.26010.3080.0666-0.198-0.98091.80030.93010.01091.99850.66380.9904-14.0555-17.0021-51.5999
181.9741-0.42692.91062.0272-1.97255.7481-0.03452.56481.6086-1.4174-0.08030.3367-1.11290.40520.40761.33720.0216-0.18471.45810.35281.17314.2898-21.5576-50.3251
191.499-1.04023.55483.4704-4.38629.7584-0.64581.55491.6634-1.04130.01210.1641-2.1129-0.12241.0022.47440.4524-0.48992.1890.62761.4594-1.3486-11.4397-51.3872
206.5297-2.6012.35921.92410.76534.11640.62491.7063-0.068-0.46-0.5274-0.1519-0.0345-0.6253-0.04030.89830.2043-0.05591.2616-0.07580.51144.2389-30.9814-39.9358
212.0144-2.29811.22463.371-0.96820.9680.03241.37752.0534-1.63830.66021.1814-1.2717-0.77421.0162.26690.4828-0.65352.41190.88891.8929-9.6387-11.0058-54.691
220.64541.01720.39132.0832-0.37612.2754-0.28581.550.6242-1.7161-0.37060.2376-0.4494-0.2998-0.63572.06640.7408-0.09262.59960.70320.91880.1599-20.2562-59.3519
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 114 )A19 - 114
2X-RAY DIFFRACTION2chain 'A' and (resid 115 through 176 )A115 - 176
3X-RAY DIFFRACTION3chain 'A' and (resid 177 through 226 )A177 - 226
4X-RAY DIFFRACTION4chain 'A' and (resid 227 through 339 )A227 - 339
5X-RAY DIFFRACTION5chain 'B' and (resid 346 through 375 )B346 - 375
6X-RAY DIFFRACTION6chain 'B' and (resid 376 through 400 )B376 - 400
7X-RAY DIFFRACTION7chain 'B' and (resid 401 through 410 )B401 - 410
8X-RAY DIFFRACTION8chain 'B' and (resid 411 through 488 )B411 - 488
9X-RAY DIFFRACTION9chain 'B' and (resid 489 through 502 )B489 - 502
10X-RAY DIFFRACTION10chain 'H' and (resid 1 through 120 )H1 - 120
11X-RAY DIFFRACTION11chain 'H' and (resid 121 through 177 )H121 - 177
12X-RAY DIFFRACTION12chain 'H' and (resid 178 through 195 )H178 - 195
13X-RAY DIFFRACTION13chain 'H' and (resid 196 through 213 )H196 - 213
14X-RAY DIFFRACTION14chain 'L' and (resid 1 through 38 )L1 - 38
15X-RAY DIFFRACTION15chain 'L' and (resid 39 through 101 )L39 - 101
16X-RAY DIFFRACTION16chain 'L' and (resid 102 through 117 )L102 - 117
17X-RAY DIFFRACTION17chain 'L' and (resid 118 through 136 )L118 - 136
18X-RAY DIFFRACTION18chain 'L' and (resid 137 through 150 )L137 - 150
19X-RAY DIFFRACTION19chain 'L' and (resid 151 through 163 )L151 - 163
20X-RAY DIFFRACTION20chain 'L' and (resid 164 through 174 )L164 - 174
21X-RAY DIFFRACTION21chain 'L' and (resid 175 through 191 )L175 - 191
22X-RAY DIFFRACTION22chain 'L' and (resid 192 through 212 )L192 - 212

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