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- PDB-6ii4: Crystal structure of H7 hemagglutinin from A/Anhui/1/2013 in comp... -

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Basic information

Entry
Database: PDB / ID: 6ii4
TitleCrystal structure of H7 hemagglutinin from A/Anhui/1/2013 in complex with a human neutralizing antibody L4A-14
Components
  • (Hemagglutinin) x 2
  • Heavy chain of L4A-14 Fab
  • Light chain of L4A-14 Fab
KeywordsIMMUNE SYSTEM / H7 haemagglutinin / receptor binding site / neutralizing antibody / protection in vivo
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
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.3 Å
AuthorsJiang, H.H. / Shi, Y. / Qi, J. / Gao, G.F.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China81621091 China
National Natural Science Foundation of China81622031 China
Chinese Academy of SciencesXDB29010000 China
CitationJournal: Nat Microbiol / Year: 2019
Title: Structure-function analysis of neutralizing antibodies to H7N9 influenza from naturally infected humans.
Authors: Huang, K.A. / Rijal, P. / Jiang, H. / Wang, B. / Schimanski, L. / Dong, T. / Liu, Y.M. / Chang, P. / Iqbal, M. / Wang, M.C. / Chen, Z. / Song, R. / Huang, C.C. / Yang, J.H. / Qi, J. / Lin, T. ...Authors: Huang, K.A. / Rijal, P. / Jiang, H. / Wang, B. / Schimanski, L. / Dong, T. / Liu, Y.M. / Chang, P. / Iqbal, M. / Wang, M.C. / Chen, Z. / Song, R. / Huang, C.C. / Yang, J.H. / Qi, J. / Lin, T.Y. / Li, A. / Powell, T.J. / Jan, J.T. / Ma, C. / Gao, G.F. / Shi, Y. / Townsend, A.R.
History
DepositionOct 3, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.2Dec 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Feb 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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
B: Hemagglutinin
C: Hemagglutinin
D: Hemagglutinin
E: Heavy chain of L4A-14 Fab
F: Light chain of L4A-14 Fab
H: Heavy chain of L4A-14 Fab
L: Light chain of L4A-14 Fab


Theoretical massNumber of molelcules
Total (without water)200,8398
Polymers200,8398
Non-polymers00
Water00
1
A: Hemagglutinin
B: Hemagglutinin
H: Heavy chain of L4A-14 Fab
L: Light chain of L4A-14 Fab

A: Hemagglutinin
B: Hemagglutinin
H: Heavy chain of L4A-14 Fab
L: Light chain of L4A-14 Fab

A: Hemagglutinin
B: Hemagglutinin
H: Heavy chain of L4A-14 Fab
L: Light chain of L4A-14 Fab


Theoretical massNumber of molelcules
Total (without water)301,25912
Polymers301,25912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-y+2,x-y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z1
2
C: Hemagglutinin
D: Hemagglutinin
E: Heavy chain of L4A-14 Fab
F: Light chain of L4A-14 Fab

C: Hemagglutinin
D: Hemagglutinin
E: Heavy chain of L4A-14 Fab
F: Light chain of L4A-14 Fab

C: Hemagglutinin
D: Hemagglutinin
E: Heavy chain of L4A-14 Fab
F: Light chain of L4A-14 Fab


Theoretical massNumber of molelcules
Total (without water)301,25912
Polymers301,25912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_865-y+3,x-y+1,z1
crystal symmetry operation3_785-x+y+2,-x+3,z1
Unit cell
Length a, b, c (Å)127.484, 127.484, 429.649
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Hemagglutinin / H7 Hemagglutinin


Mass: 34553.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A024CX39
#2: Protein Hemagglutinin / H7 Hemagglutinin


Mass: 19273.064 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A0K1LUI9
#3: Antibody Heavy chain of L4A-14 Fab


Mass: 23813.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#4: Antibody Light chain of L4A-14 Fab


Mass: 22780.010 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
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: 3.35 Å3/Da / Density % sol: 63.23 %
Crystal growTemperature: 291.15 K / Method: evaporation / pH: 7
Details: 0.2M Ammonium citrate tribasic pH7.0, 20%, 30 w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 39511 / % possible obs: 99.9 % / Redundancy: 6 % / Biso Wilson estimate: 78.7 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.055 / Rsym value: 0.123 / Net I/σ(I): 14.8
Reflection shellResolution: 3.3→3.42 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1-2575_1692: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 3.3→41.044 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.8
RfactorNum. reflection% reflectionSelection details
Rfree0.2762 1981 5.02 %Cross-validaCross-validation methodtion method
Rwork0.2267 ---
obs0.2292 39479 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.3→41.044 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14016 0 0 0 14016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214334
X-RAY DIFFRACTIONf_angle_d0.60719450
X-RAY DIFFRACTIONf_dihedral_angle_d16.3045252
X-RAY DIFFRACTIONf_chiral_restr0.0412124
X-RAY DIFFRACTIONf_plane_restr0.0042544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2884-3.37060.32151530.29712629X-RAY DIFFRACTION99
3.3706-3.46170.31381380.27952670X-RAY DIFFRACTION100
3.4617-3.56350.31941360.27012708X-RAY DIFFRACTION100
3.5635-3.67840.28921500.25992672X-RAY DIFFRACTION100
3.6784-3.80980.27791580.2572645X-RAY DIFFRACTION100
3.8098-3.96220.32571510.24932703X-RAY DIFFRACTION100
3.9622-4.14240.27081250.23032696X-RAY DIFFRACTION100
4.1424-4.36050.28191440.20282664X-RAY DIFFRACTION100
4.3605-4.63340.23141400.19392677X-RAY DIFFRACTION100
4.6334-4.99060.23961360.19642683X-RAY DIFFRACTION100
4.9906-5.49170.24951540.20222707X-RAY DIFFRACTION100
5.4917-6.2840.30451440.23562676X-RAY DIFFRACTION100
6.284-7.90790.2831260.25062698X-RAY DIFFRACTION100
7.9079-41.04740.26531260.20722670X-RAY DIFFRACTION99
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)
10.24360.0759-0.3891-0.13430.42244.34260.01570.02480.0343-0.0596-0.11220.0224-0.3775-0.6813-0.00020.4610.0529-0.00840.4729-0.0140.4846114.368288.9511-24.6138
2-0.0815-0.1265-0.50380.6944-0.45941.4104-0.03560.01690.0915-0.0551-0.05840.0772-0.721-0.4774-0.00860.4117-0.0367-0.01540.41720.09440.3443124.312185.977-73.8334
30.03260.1335-0.10710.46640.9632.4956-0.061-0.2147-0.21450.37620.0352-0.11070.09830.42850.0021.0090.0761-0.1040.76280.1240.6677134.3593128.298541.5443
4-0.233-0.22810.2742-0.7710.26920.32480.1561-0.3067-0.06090.25720.175-0.21760.69040.43130.00852.0302-0.1617-0.32892.03160.12780.7363136.9385138.167290.8222
52.32750.65260.12522.25580.90981.38530.0767-0.0434-0.31490.1224-0.03470.00530.64250.0057-00.7060.12560.05980.30830.02040.6456133.2084112.7294-8.4592
61.5473-0.2135-1.15240.66211.38052.6568-0.98260.53120.2777-2.05261.0345-0.72290.82441.48330.08431.9585-0.50090.28221.54130.02851.0778141.8854120.4601-47.5681
70.69240.84620.69661.71090.18511.6357-0.16690.2271-0.0017-0.0187-0.0139-0.3673-0.4580.489700.6041-0.02570.03520.60680.02370.9254142.4607133.2897-9.9162
80.1656-0.0326-0.3350.2637-0.49091.2114-1.2741.59230.648-1.29640.8927-0.0198-0.86790.72250.00211.5339-0.5023-0.16921.33530.26881.4208135.4096133.1259-39.6554
92.0617-0.04260.11521.76510.01591.644-0.1110.40010.0528-0.14180.52870.21990.9277-2.08590.06410.09880.72910.09070.6034-0.10240.4987100.849696.421225.309
101.44710.2343-1.23540.7001-0.50960.9504-0.04-1.61760.34650.52130.3206-0.0403-1.86940.19050.00681.26520.1823-0.01931.7815-0.30510.8994112.4495100.380364.2384
111.2908-0.1548-0.61740.8397-0.71192.6001-0.0706-0.10010.0850.0691-0.1734-0.2759-0.60240.3084-00.44690.0296-0.03420.2846-0.02410.5318123.41193.489727.0861
120.7892-0.21370.64690.29880.29151.64150.2187-1.6359-0.57570.3679-0.7218-0.4801-0.77550.6748-0.01220.7734-0.02970.0041.06390.28561.1712119.5687.819256.7428
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 317)
2X-RAY DIFFRACTION2chain 'B' and (resid 5 through 170 )
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 317 )
4X-RAY DIFFRACTION4chain 'D' and (resid 5 through 170 )
5X-RAY DIFFRACTION5chain 'E' and (resid 1 through 119 )
6X-RAY DIFFRACTION6chain 'E' and (resid 120 through 225 )
7X-RAY DIFFRACTION7chain 'F' and (resid 1 through 117 )
8X-RAY DIFFRACTION8chain 'F' and (resid 118 through 212 )
9X-RAY DIFFRACTION9chain 'H' and (resid 1 through 119 )
10X-RAY DIFFRACTION10chain 'H' and (resid 120 through 225 )
11X-RAY DIFFRACTION11chain 'L' and (resid 1 through 119 )
12X-RAY DIFFRACTION12chain 'L' and (resid 120 through 212 )

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