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- PDB-7fah: Immune complex of head region of CA09 HA and neutralizing antibod... -

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Basic information

Entry
Database: PDB / ID: 7fah
TitleImmune complex of head region of CA09 HA and neutralizing antibody 12H5
Components
  • Hemagglutinin
  • Light chain of antibody 12H5
  • heavy chain of antibody 12H5
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Influenza virus / HA / Receptor binding site / neutralizing antibody / VIRAL 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 / metal ion binding / membrane
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.151 Å
AuthorsLi, T.T. / Xue, W.H. / Gu, Y. / Li, S.W.
CitationJournal: Nat Commun / Year: 2022
Title: Identification of a cross-neutralizing antibody that targets the receptor binding site of H1N1 and H5N1 influenza viruses.
Authors: Tingting Li / Junyu Chen / Qingbing Zheng / Wenhui Xue / Limin Zhang / Rui Rong / Sibo Zhang / Qian Wang / Minqing Hong / Yuyun Zhang / Lingyan Cui / Maozhou He / Zhen Lu / Zhenyong Zhang / ...Authors: Tingting Li / Junyu Chen / Qingbing Zheng / Wenhui Xue / Limin Zhang / Rui Rong / Sibo Zhang / Qian Wang / Minqing Hong / Yuyun Zhang / Lingyan Cui / Maozhou He / Zhen Lu / Zhenyong Zhang / Xin Chi / Jinjin Li / Yang Huang / Hong Wang / Jixian Tang / Dong Ying / Lizhi Zhou / Yingbin Wang / Hai Yu / Jun Zhang / Ying Gu / Yixin Chen / Shaowei Li / Ningshao Xia /
Abstract: Influenza A viruses pose a significant threat globally each year, underscoring the need for a vaccine- or antiviral-based broad-protection strategy. Here, we describe a chimeric monoclonal antibody, ...Influenza A viruses pose a significant threat globally each year, underscoring the need for a vaccine- or antiviral-based broad-protection strategy. Here, we describe a chimeric monoclonal antibody, C12H5, that offers neutralization against seasonal and pandemic H1N1 viruses, and cross-protection against some H5N1 viruses. Notably, C12H5 mAb offers broad neutralizing activity against H1N1 and H5N1 viruses by controlling virus entry and egress, and offers protection against H1N1 and H5N1 viral challenge in vivo. Through structural analyses, we show that C12H5 engages hemagglutinin (HA), the major surface glycoprotein on influenza, at a distinct epitope overlapping the receptor binding site and covering the 140-loop. We identified eight highly conserved (~90%) residues that are essential for broad H1N1 recognition, with evidence of tolerance for Asp or Glu at position 190; this site is a molecular determinant for human or avian host-specific recognition and this tolerance endows C12H5 with cross-neutralization potential. Our results could benefit the development of antiviral drugs and the design of broad-protection influenza vaccines.
History
DepositionJul 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Refinement description / Category: citation / citation_author / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 30, 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
H: heavy chain of antibody 12H5
L: Light chain of antibody 12H5
B: Hemagglutinin
C: heavy chain of antibody 12H5
D: Light chain of antibody 12H5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,64410
Polymers217,8116
Non-polymers8334
Water00
1
A: Hemagglutinin
H: heavy chain of antibody 12H5
L: Light chain of antibody 12H5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,3225
Polymers108,9063
Non-polymers4162
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hemagglutinin
C: heavy chain of antibody 12H5
D: Light chain of antibody 12H5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,3225
Polymers108,9063
Non-polymers4162
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.740, 51.122, 168.248
Angle α, β, γ (deg.)90.000, 106.900, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain D
21chain L
12chain H
22chain C
13chain A
23chain B

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPARGARGchain DDF1 - 2151 - 215
21ASPASPARGARGchain LLC1 - 2151 - 215
12GLNGLNARGARGchain HHB1 - 2171 - 217
22GLNGLNARGARGchain CCE1 - 2171 - 217
13VALVALASNASNchain AAA56 - 26948 - 261
23VALVALASNASNchain BBD56 - 26948 - 261

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Hemagglutinin


Mass: 61584.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain swl A/California/04/2009 H1N1)
Gene: HA / Cell line (production host): Tn5 cell / Production host: Trichoplusia ni / References: UniProt: C3W5S1
#2: Antibody heavy chain of antibody 12H5


Mass: 23370.369 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody Light chain of antibody 12H5


Mass: 23950.232 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#4: 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.: 2 / Source method: obtained synthetically / 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
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
Has ligand of interestN
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: 2.04 Å3/Da / Density % sol: 39.57 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES pH 6.5, 13% (w/v) PEG 2000

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Data collection

DiffractionMean temperature: 123.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. obs: 30642 / % possible obs: 99.8 % / Redundancy: 11.8 % / Biso Wilson estimate: 63.04 Å2 / CC1/2: 0.862 / Rpim(I) all: 0.077 / Rsym value: 0.188 / Net I/σ(I): 19.2
Reflection shellResolution: 3.15→3.2 Å / Num. unique obs: 2709 / Rsym value: 0.926

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LZG, 1C1E

3lzg

1c1e


Resolution: 3.151→38.606 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2895 1492 4.88 %
Rwork0.2663 29099 -
obs0.2674 30591 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 251.25 Å2 / Biso mean: 107.3251 Å2 / Biso min: 26.29 Å2
Refinement stepCycle: final / Resolution: 3.151→38.606 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10014 0 52 0 10066
Biso mean--83.78 --
Num. residues----1292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310344
X-RAY DIFFRACTIONf_angle_d0.67614080
X-RAY DIFFRACTIONf_chiral_restr0.0451530
X-RAY DIFFRACTIONf_plane_restr0.0041808
X-RAY DIFFRACTIONf_dihedral_angle_d13.1216184
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11D2554X-RAY DIFFRACTION3.903TORSIONAL
12L2554X-RAY DIFFRACTION3.903TORSIONAL
21H2497X-RAY DIFFRACTION3.903TORSIONAL
22C2497X-RAY DIFFRACTION3.903TORSIONAL
31A2655X-RAY DIFFRACTION3.903TORSIONAL
32B2655X-RAY DIFFRACTION3.903TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.151-3.25240.35211160.3368230487
3.2524-3.36860.37021420.31112653100
3.3686-3.50340.32321470.29762638100
3.5034-3.66280.32121470.28652643100
3.6628-3.85570.31661290.27332645100
3.8557-4.0970.27581420.25732647100
4.097-4.41290.24861370.24862668100
4.4129-4.85630.26281360.24032657100
4.8563-5.55720.24381040.24232723100
5.5572-6.99470.28621340.27882721100
6.9947-38.6060.28761580.25442800100
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)
10.0186-0.02260.04821.6131-0.17250.0696-0.0793-0.0302-0.5710.59370.2360.11330.11370.19280.03540.19960.0122-0.01680.49680.0260.565939.49427.6025164.4388
20.1703-0.2561-0.2191.2946-0.57010.6442-0.0785-0.14460.11370.20860.1881-0.5523-0.1715-0.0060.08070.28930.0002-0.10760.3323-0.03280.467948.775723.5256167.0465
30.55110.0524-0.26410.4741-0.20160.2676-0.05630.2580.34710.09150.4602-0.09350.0508-0.2650.16370.3115-0.0134-0.05630.2845-0.02310.377142.642922.5035165.9972
40.02810.03520.05140.0110.05520.07020.11190.0447-0.12230.26380.1379-0.80670.45040.47010.00290.97550.3080.13620.98430.13171.017767.8053-7.1158192.5332
50.1516-0.0898-0.01840.2026-0.04270.406-0.198-0.3519-0.46540.52360.1810.7140.09330.0489-0.05330.64370.26450.07760.6640.13610.529260.53951.8639186.3962
60.1302-0.0604-0.0960.01840.0210.15350.0058-0.13550.0459-0.01180.01380.08440.20510.2741-0.00450.65180.37960.07690.84980.11350.843367.24730.6235183.4594
70.0678-0.07410.00620.09720.0118-0.0133-0.2485-0.22-0.01470.52080.1442-0.37010.3530.6965-0.01650.99170.3241-0.06521.1160.34680.679670.61671.7551193.3371
80.5108-0.09630.56960.92630.40951.1969-0.4777-0.3643-0.29320.3562-0.37560.2821-0.2362-0.2081-0.72191.14280.37840.23111.20710.54450.604764.5189-2.7684195.9921
90.0165-0.01960.01690.0049-0.01660.0146-0.0540.23610.04950.1088-0.40380.0710.07480.1270.00012.25750.08060.30042.50280.79981.454965.527-17.2136229.5624
100.065-0.0014-0.03750.3010.24880.2225-0.22240.0241-0.03450.1417-0.58760.28240.26030.0582-0.06292.19280.44290.17251.80160.51811.038464.5055-13.5361215.2516
110.0206-0.02180.01930.03560.00350.0258-0.0367-0.0236-0.02820.3487-0.07630.10180.0577-0.0659-01.87460.55540.09591.94960.75712.115970.6171-9.268216.0408
12-0.0036-0.0067-0.01570.001-0.01340.0104-0.04160.13440.0250.18050.02110.0454-0.02410.081202.30610.23090.02122.19850.89351.960.9805-22.6774220.4675
130.00240.0020.012-0.00530.00640.0097-0.05090.17320.07530.00450.09070.026-0.05550.060202.16530.20250.01331.28730.1171.548169.3161-22.4237214.8018
140.51680.29970.4530.36270.4550.5813-0.4751-0.50930.39580.53410.11930.4221-0.59160.0343-0.23630.8550.330.13130.7458-0.11480.476851.390112.8893202.7863
150.04390.0744-0.06320.0635-0.0530.089-0.11030.06260.1558-0.2333-0.22860.01750.2061-0.2961-0.00012.50720.39080.28732.61960.60681.169771.749-6.5418227.5393
160.06390.0240.09450.00820.04220.0814-0.124-0.3807-0.04180.1563-0.1562-0.0424-0.17220.1766-0.2832.22760.5760.37272.36570.55780.504671.0663-4.2309228.0403
170.07-0.1662-0.08561.64820.30180.1326-0.19710.04150.39290.43640.24380.10910.0667-0.11330.00920.2529-0.04680.03070.47980.00320.540324.2704-2.2565164.421
180.24720.22110.1130.9274-0.06810.321-0.2253-0.05210.2414-0.13210.30080.88670.2924-0.05660.05290.3503-0.01460.10140.34360.03550.695311.9657-14.7229166.0952
190.8848-0.04160.60731.36660.75580.7532-0.17620.1973-0.2860.20650.3390.03280.12610.2330.07180.28660.04340.0710.30450.0250.518320.7583-20.2296167.0731
201.1344-0.0051-0.69131.6394-0.33180.7052-0.7028-0.61510.54690.37810.0131-0.5663-0.3916-0.2584-1.4640.81670.4605-0.15160.8781-0.25190.5619-1.33075.5938189.531
210.26740.3562-0.24220.3969-0.29110.2195-0.264-0.37330.58060.3007-0.7142-0.417-0.2588-0.1335-0.34612.17660.9665-0.5722.0898-0.68561.369-1.703219.2773219.6631
220.0028-0.00470.0430.02650.01290.1581-0.37220.3602-0.19380.5695-0.1265-0.1105-0.1719-0.0767-0.01322.74811.0462-0.68892.1977-0.77411.9235-3.902422.54217.4151
230.53670.1008-0.74680.592-0.8712.3842-0.9663-0.4215-0.16490.5256-0.0519-0.7650.4798-0.3691-1.66420.93790.6257-0.31360.71550.1280.213412.0031-7.8963202.817
240.0241-0.0024-0.0453-0.023-0.01660.1713-0.3534-0.31190.0109-0.1934-0.0207-0.095-0.1069-0.0716-0.42392.85011.3523-0.48883.1175-1.0727-0.6099-8.49279.5305227.8942
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 56 through 111 )A56 - 111
2X-RAY DIFFRACTION2chain 'A' and (resid 112 through 219 )A112 - 219
3X-RAY DIFFRACTION3chain 'A' and (resid 220 through 269 )A220 - 269
4X-RAY DIFFRACTION4chain 'H' and (resid 1 through 17 )H1 - 17
5X-RAY DIFFRACTION5chain 'H' and (resid 18 through 60 )H18 - 60
6X-RAY DIFFRACTION6chain 'H' and (resid 61 through 83 )H61 - 83
7X-RAY DIFFRACTION7chain 'H' and (resid 84 through 98 )H84 - 98
8X-RAY DIFFRACTION8chain 'H' and (resid 99 through 123 )H99 - 123
9X-RAY DIFFRACTION9chain 'H' and (resid 124 through 138 )H124 - 138
10X-RAY DIFFRACTION10chain 'H' and (resid 139 through 172 )H139 - 172
11X-RAY DIFFRACTION11chain 'H' and (resid 173 through 188 )H173 - 188
12X-RAY DIFFRACTION12chain 'H' and (resid 189 through 203 )H189 - 203
13X-RAY DIFFRACTION13chain 'H' and (resid 204 through 217 )H204 - 217
14X-RAY DIFFRACTION14chain 'L' and (resid 1 through 117 )L1 - 117
15X-RAY DIFFRACTION15chain 'L' and (resid 118 through 159 )L118 - 159
16X-RAY DIFFRACTION16chain 'L' and (resid 160 through 215 )L160 - 215
17X-RAY DIFFRACTION17chain 'B' and (resid 56 through 111 )B56 - 111
18X-RAY DIFFRACTION18chain 'B' and (resid 112 through 180 )B112 - 180
19X-RAY DIFFRACTION19chain 'B' and (resid 181 through 269 )B181 - 269
20X-RAY DIFFRACTION20chain 'C' and (resid 1 through 123 )C1 - 123
21X-RAY DIFFRACTION21chain 'C' and (resid 124 through 172 )C124 - 172
22X-RAY DIFFRACTION22chain 'C' and (resid 173 through 217 )C173 - 217
23X-RAY DIFFRACTION23chain 'D' and (resid 1 through 117 )D1 - 117
24X-RAY DIFFRACTION24chain 'D' and (resid 118 through 215 )D118 - 215

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