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- PDB-6ii9: Crystal structure of H7 hemagglutinin from A/Anhui/1/2013 in comp... -

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Basic information

Entry
Database: PDB / ID: 6ii9
TitleCrystal structure of H7 hemagglutinin from A/Anhui/1/2013 in complex with a human neutralizing antibody L3A-44
Components
  • (Hemagglutinin) x 2
  • Heavy chain of L3A-44 Fab
  • Light chain of L3A-44 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 / 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
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.5 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 1.1Dec 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 1.2Feb 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 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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: Hemagglutinin
F: Hemagglutinin
H: Heavy chain of L3A-44 Fab
L: Light chain of L3A-44 Fab
M: Heavy chain of L3A-44 Fab
N: Light chain of L3A-44 Fab
P: Heavy chain of L3A-44 Fab
Q: Light chain of L3A-44 Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,91715
Polymers299,25312
Non-polymers6643
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area47400 Å2
ΔGint-223 kcal/mol
Surface area109580 Å2
Unit cell
Length a, b, c (Å)178.457, 184.906, 188.990
Angle α, β, γ (deg.)90.00, 106.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Hemagglutinin / / H7 Hemagglutinin


Mass: 34553.016 Da / Num. of mol.: 3
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: 19647.502 Da / Num. of mol.: 3
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 L3A-44 Fab


Mass: 23412.020 Da / Num. of mol.: 3
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 L3A-44 Fab


Mass: 22138.480 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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: 5 Å3/Da / Density % sol: 75.39 %
Crystal growTemperature: 291.15 K / Method: evaporation / pH: 7.5
Details: 0.2M Magnesium chloride hexahydrate, 0.1M HEPES pH 7.5, 22% w/v poly (acrylic acid sodium salt) 5100

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 73039 / % possible obs: 98 % / Redundancy: 4.1 % / Biso Wilson estimate: 77.9 Å2 / CC1/2: 0.977 / Rpim(I) all: 0.111 / Rsym value: 0.199 / Net I/σ(I): 8.4
Reflection shellResolution: 3.5→3.63 Å / Mean I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 3.5→43.841 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.64
RfactorNum. reflection% reflection
Rfree0.2338 3688 5.06 %
Rwork0.2007 --
obs0.2024 72894 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.5→43.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20897 0 42 0 20939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621431
X-RAY DIFFRACTIONf_angle_d0.99429116
X-RAY DIFFRACTIONf_dihedral_angle_d17.4317792
X-RAY DIFFRACTIONf_chiral_restr0.0523204
X-RAY DIFFRACTIONf_plane_restr0.0063791
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4814-3.52720.3908970.32861990X-RAY DIFFRACTION73
3.5272-3.57550.35611370.32112745X-RAY DIFFRACTION99
3.5755-3.62660.29841460.3062699X-RAY DIFFRACTION99
3.6266-3.68070.34981380.30032698X-RAY DIFFRACTION99
3.6807-3.73810.33591620.29042670X-RAY DIFFRACTION99
3.7381-3.79940.3161590.27812688X-RAY DIFFRACTION99
3.7994-3.86490.40761420.27652690X-RAY DIFFRACTION98
3.8649-3.93510.29921360.2722724X-RAY DIFFRACTION99
3.9351-4.01070.30361540.24982716X-RAY DIFFRACTION99
4.0107-4.09250.27541360.23752656X-RAY DIFFRACTION99
4.0925-4.18150.26271580.22122693X-RAY DIFFRACTION99
4.1815-4.27870.24831310.19892746X-RAY DIFFRACTION99
4.2787-4.38560.2311570.19162657X-RAY DIFFRACTION98
4.3856-4.5040.2061400.18012701X-RAY DIFFRACTION98
4.504-4.63640.21081470.1752693X-RAY DIFFRACTION98
4.6364-4.78590.18921550.16282691X-RAY DIFFRACTION98
4.7859-4.95670.17621330.16052717X-RAY DIFFRACTION98
4.9567-5.15490.21440.15832682X-RAY DIFFRACTION98
5.1549-5.38910.19171270.16332708X-RAY DIFFRACTION98
5.3891-5.67270.23081470.17732669X-RAY DIFFRACTION98
5.6727-6.02720.24661560.17512678X-RAY DIFFRACTION98
6.0272-6.49120.19041200.18332694X-RAY DIFFRACTION97
6.4912-7.1420.21391390.18682715X-RAY DIFFRACTION97
7.142-8.16960.20061470.16672624X-RAY DIFFRACTION96
8.1696-10.2710.14881310.13632700X-RAY DIFFRACTION97
10.271-43.84480.18731490.18562562X-RAY DIFFRACTION91
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)
10.63580.12510.23920.01590.06460.26280.12970.23220.03720.0838-0.03140.02640.09720.0923-00.60260.0110.02190.60670.01540.606510.8084-65.426831.4965
20.1173-0.03130.12150.26250.29470.3905-0.10990.19380.13650.0207-0.0041-0.0537-0.0059-0.1643-00.3957-0.06930.00550.81890.05340.4252-34.8478-66.25546.821
30.32690.08130.2258-0.0556-0.03130.53680.2202-0.0819-0.1952-0.0128-0.0562-0.07510.262-0.2204-0.02570.5364-0.06770.02420.4030.00990.4247-6.141-83.363452.4191
40.57510.48430.05490.58650.2990.2570.2236-0.0257-0.04540.1905-0.0280.07630.2702-0.46220.19680.3319-0.1440.05670.93260.06930.4248-46.9515-74.041122.6737
50.61620.06650.4690.1780.12620.5466-0.07450.01680.13850.0334-0.04260.0558-0.0852-0.145800.56120.01930.04860.47840.00120.5487-5.9447-50.537355.5748
60.20050.1478-0.04860.1633-0.03370.0512-0.004-0.07020.2082-0.0294-0.05350.0357-0.1411-0.369300.510.1735-0.07860.9069-0.00610.5999-44.2338-52.951920.5692
70.25810.0042-0.06730.1481-0.12760.11520.22980.4039-0.06460.1508-0.2297-0.07420.02410.2057-0.00020.46580.1346-0.01960.8876-0.11050.499157.136-76.055538.9721
80.3636-0.0299-0.07350.0718-0.10050.16360.23981.0323-0.48170.27520.2084-0.2640.18190.36210.0170.86590.2834-0.22641.0299-0.29311.209282.7646-106.133748.7953
90.15770.0168-0.13820.261-0.15980.19680.26950.2715-0.42150.095-0.12810.39820.1108-0.1834-00.72120.1251-0.0960.8414-0.28250.950744.6563-94.734742.4293
100.26310.0368-0.15410.1526-0.13040.17760.2808-0.0088-0.30270.3798-0.20650.0873-0.17420.067300.89570.0756-0.13610.8891-0.14721.136668.7061-103.657257.2298
110.2509-0.0407-0.02880.1344-0.22270.39120.1459-0.0479-0.1297-0.2574-0.0095-0.00410.3263-0.055600.6867-0.0407-0.03610.440.10150.69318.9868-98.454190.5396
120.1731-0.1287-0.05670.2185-0.02510.160.2747-0.7964-0.5207-0.079-0.0577-0.0149-0.0082-0.41380.00950.7694-0.09510.02531.4290.13840.678823.7498-92.185130.2106
130.2360.00360.00530.43580.07470.3677-0.0091-0.06130.2153-0.1608-0.0374-0.1452-0.276-0.2243-00.5639-0.01060.03210.63930.06350.61885.9452-80.772296.02
140.06980.0258-0.10340.1919-0.04850.1450.4029-0.44420.2606-0.044-0.4126-0.0901-0.1739-0.2884-00.8466-0.07070.09021.16030.00310.963423.8439-78.4138120.5839
150.26390.27250.01030.27350.07810.4276-0.1498-0.16420.25540.0095-0.0070.15760.0066-0.0274-00.69050.0349-0.04660.3889-0.04610.690626.7657-28.412982.3675
160.33870.1070.17230.25240.05470.3581-0.6279-0.04550.82050.33470.0382-0.1865-0.202-0.1347-0.06430.763-0.2356-0.2050.76910.18461.026360.2514-5.898979.1366
170.35770.0879-0.17960.2031-0.12230.2445-0.31680.38080.0859-0.17310.10280.1272-0.10340.0795-0.00280.778-0.1484-0.07910.3770.11230.602431.8439-27.076960.3709
180.15280.1135-0.02760.14190.05740.1097-0.40510.2630.39910.0964-0.045-0.17020.24140.474500.9519-0.118-0.03940.79660.16010.814758.8156-19.996970.5047
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:317 )A1 - 317
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1:170 )B1 - 170
3X-RAY DIFFRACTION3( CHAIN C AND RESID 1:317 )C1 - 317
4X-RAY DIFFRACTION4( CHAIN D AND RESID 1:170 )D1 - 170
5X-RAY DIFFRACTION5( CHAIN E AND RESID 1:316 )E1 - 316
6X-RAY DIFFRACTION6( CHAIN F AND RESID 1:170 )F1 - 170
7X-RAY DIFFRACTION7( CHAIN H AND RESID 2:127 )H2 - 127
8X-RAY DIFFRACTION8( CHAIN H AND RESID 128:222 )H128 - 222
9X-RAY DIFFRACTION9( CHAIN L AND RESID 3:118 )L3 - 118
10X-RAY DIFFRACTION10( CHAIN L AND RESID 119:214 )L119 - 214
11X-RAY DIFFRACTION11( CHAIN M AND RESID 2:127 )M2 - 127
12X-RAY DIFFRACTION12( CHAIN M AND RESID 128:222 )M128 - 222
13X-RAY DIFFRACTION13( CHAIN N AND RESID 3:118 )N3 - 118
14X-RAY DIFFRACTION14( CHAIN N AND RESID 119:214 )N119 - 214
15X-RAY DIFFRACTION15( CHAIN P AND RESID 2:127 )P2 - 127
16X-RAY DIFFRACTION16( CHAIN P AND RESID 128:222 )P128 - 222
17X-RAY DIFFRACTION17( CHAIN Q AND RESID 3:118 )Q3 - 118
18X-RAY DIFFRACTION18( CHAIN Q AND RESID 119:214 )Q119 - 214

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