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- PDB-4xnq: Antibody hemagglutinin Complexes -

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Basic information

Entry
Database: PDB / ID: 4xnq
TitleAntibody hemagglutinin Complexes
Components
  • H5.3 Light chain
  • H5.3 heavy chain
  • Influenza H5 HA head domain VietNam rdt mutations
KeywordsViral protein/Immune system / Antibody / hemagglutinin / neutralization / 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 / 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 / identical protein binding
Similarity search - Function
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 / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like ...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 / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsSpiller, B.W. / Winarski, K.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272200900047C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R21 AI092268 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Vaccine-elicited antibody that neutralizes H5N1 influenza and variants binds the receptor site and polymorphic sites.
Authors: Winarski, K.L. / Thornburg, N.J. / Yu, Y. / Sapparapu, G. / Crowe, J.E. / Spiller, B.W.
History
DepositionJan 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Non-polymer description
Revision 1.2Jul 29, 2015Group: Database references
Revision 1.3Aug 12, 2015Group: Database references
Revision 1.4Sep 9, 2015Group: Source and taxonomy
Revision 1.5Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.6Dec 11, 2019Group: Author supporting evidence / Data collection / Database references
Category: chem_comp / citation ...chem_comp / citation / citation_author / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
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_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_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 2.1Mar 30, 2022Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_audit_support / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H5.3 Light chain
B: H5.3 heavy chain
D: Influenza H5 HA head domain VietNam rdt mutations
L: H5.3 Light chain
H: H5.3 heavy chain
C: Influenza H5 HA head domain VietNam rdt mutations
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,7997
Polymers141,2286
Non-polymers5711
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12790 Å2
ΔGint-57 kcal/mol
Surface area53470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)250.400, 51.178, 127.702
Angle α, β, γ (deg.)90.00, 100.17, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody H5.3 Light chain


Mass: 22327.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): hybridoma / Production host: Homo sapiens (human)
#2: Antibody H5.3 heavy chain


Mass: 23964.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): hybridoma / Production host: Homo sapiens (human)
#3: Protein Influenza H5 HA head domain VietNam rdt mutations


Mass: 24321.535 Da / Num. of mol.: 2 / Fragment: UNP residues 74-285
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Vietnam/1203/2004(H5N1) / Production host: Escherichia coli (E. coli) / References: UniProt: H8PCX0, UniProt: Q6DQ33*PLUS
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 2.88 Å3/Da / Density % sol: 57.22 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 200 mM ammonium sulfate, 100 mM HEPES pH 7.5, 25% PEG 3350
Temp details: 294

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.00394 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00394 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 97220 / Num. obs: 97220 / % possible obs: 96.9 % / Redundancy: 4 % / Rsym value: 0.048 / Net I/σ(I): 26.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.5 / % possible all: 53.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1760)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.001→33.084 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2252 1999 2.06 %
Rwork0.191 --
obs0.1917 97220 89.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.001→33.084 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9616 0 38 403 10057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089927
X-RAY DIFFRACTIONf_angle_d1.13413543
X-RAY DIFFRACTIONf_dihedral_angle_d12.083529
X-RAY DIFFRACTIONf_chiral_restr0.0491530
X-RAY DIFFRACTIONf_plane_restr0.0071714
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.001-2.0510.379800.33463778X-RAY DIFFRACTION50
2.051-2.10640.3544960.30164619X-RAY DIFFRACTION62
2.1064-2.16840.33031200.28065689X-RAY DIFFRACTION76
2.1684-2.23840.31341520.27657247X-RAY DIFFRACTION96
2.2384-2.31840.28251520.25257203X-RAY DIFFRACTION96
2.3184-2.41120.2941520.24937238X-RAY DIFFRACTION96
2.4112-2.52090.26611500.24197211X-RAY DIFFRACTION96
2.5209-2.65370.28261530.24157278X-RAY DIFFRACTION96
2.6537-2.81990.26451540.23257332X-RAY DIFFRACTION97
2.8199-3.03750.30551560.22817435X-RAY DIFFRACTION98
3.0375-3.34290.22521560.21317417X-RAY DIFFRACTION98
3.3429-3.8260.20861570.18337497X-RAY DIFFRACTION98
3.826-4.8180.1851590.13857571X-RAY DIFFRACTION99
4.818-33.08870.17011620.14737706X-RAY DIFFRACTION98
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)
13.739-0.96370.32872.0488-0.88034.0471-0.2093-0.37850.07380.10620.19210.0857-0.4072-1.12390.03130.56260.16130.12910.6306-0.06460.3752461.857228.4272297.0076
21.91550.06180.55992.2532.60357.1089-0.3197-0.65320.17150.11860.31310.0068-0.0993-0.39330.02120.42630.25570.05070.82890.10270.3951445.062430.5505270.855
33.10840.78090.0114.5381.64517.9224-0.254-0.4773-0.17230.2480.20280.12530.5215-0.58480.10020.47460.22910.09250.79610.15220.3657445.28225.6253271.3959
43.07731.10072.70891.79810.80277.9954-0.05630.2832-0.2368-0.4929-0.115-0.0953-0.8765-0.58610.19080.55710.1170.09260.3816-0.05540.3984478.149128.8471275.7417
52.7444-0.1830.39561.8478-0.49212.5218-0.2653-0.028-0.06730.13270.0512-0.0329-0.048-0.25450.20060.50190.06750.1230.3022-0.02150.3361477.778724.6983285.3755
64.2252-0.27611.40861.1725-0.31152.0767-0.02870.0279-0.3532-0.2124-0.06480.16060.3791-0.15780.01480.67090.00870.19190.3139-0.05730.5295481.199515.602284.0212
71.7617-0.04350.68891.6271-0.6263.1166-0.11680.1156-0.19640.0779-0.0315-0.0158-0.0786-0.19520.13260.58360.05710.14320.2789-0.0360.3729477.955122.9859284.8703
82.01440.05182.59540.3233-0.85783.9013-0.25430.00750.11080.160.2290.1118-0.2508-0.358-0.00930.53180.11240.10560.5343-0.0210.371460.124132.1247269.1808
91.1147-0.37881.32891.8852-1.82993.8777-0.3955-0.47160.15770.29190.58190.2004-0.5143-0.107-0.1040.53460.07810.07830.6628-0.12580.4429455.477338.8439265.1949
108.3648-1.53221.24266.89530.09936.3198-0.07550.03680.5193-0.09540.29960.6753-0.9253-0.5562-0.20010.64740.12340.08620.57170.0160.3496448.763441.9952259.4589
115.8933-3.0497-2.66736.90536.32315.8660.00930.63291.5361-0.7088-0.1561-2.0008-0.50661.7630.08710.49270.03260.1911.00590.19740.7537498.19145.0923312.1806
125.9091-6.5995-2.32678.41294.14318.5644-0.05-0.84410.48760.5570.4558-0.86760.74441.4851-0.36480.52990.04620.01090.8635-0.00280.6165498.13612.5853309.0859
134.3865-1.89580.81076.965-2.78757.74690.0543-0.9260.62880.5831-0.3266-1.0886-0.1921.59480.29710.5676-0.09880.01881.0198-0.07550.4654494.58275.6929318.8252
143.2009-2.04450.77945.6418-3.12336.72380.41750.2315-0.0902-0.1229-0.25740.52570.4745-0.3805-0.23830.6443-0.00450.13460.4033-0.09930.4022478.02246.6085305.8375
155.4021-2.9426-0.39053.8545-1.526.7923-0.0197-0.5853-0.04190.14510.31030.17430.1707-0.1662-0.30970.5462-0.03930.07930.4374-0.01960.2777477.80354.2477319.1875
162.8143-2.03440.52848.0284-2.25686.3891-0.2003-0.1461-0.1087-0.01850.10950.1935-0.5091-0.0070.07090.4001-0.03240.08160.22010.00260.3498499.300114.4915255.4826
173.62471.761.775.64212.39374.7283-0.1145-0.1047-0.07530.7514-0.02350.34480.3976-0.35320.14210.81410.02220.17850.4509-0.02330.3371485.069713.096228.118
182.3926-2.1186-0.1866.77940.42914.9160.06140.0592-0.1308-0.84740.1140.02910.40430.5229-0.20160.60620.03640.14470.2885-0.01220.3964507.827-5.0201250.2595
192.1552-1.20472.4072-0.214-0.70372.37220.46880.5079-0.1061-0.30140.037-0.03891.28981.0338-0.54360.9169-0.00860.13950.4118-0.0120.3835506.39160.6853239.2246
206.391-4.1837-1.25888.50142.45747.3176-0.03080.13340.36170.11210.2255-0.4744-0.12560.2955-0.19420.54680.00880.12040.4263-0.05090.3393494.561313.5691214.652
215.44073.01081.28741.68430.72130.29740.72131.4122-0.9141-0.128-0.3492-1.70481.42531.6085-0.14041.0670.55870.09920.93430.0760.8127509.8878-15.7641287.8659
226.8477-0.80412.90616.349-0.36444.12320.4655-0.6844-0.48530.4738-0.9342-1.19621.49010.96620.26051.27170.4860.06530.96940.21240.706507.433-17.0522288.3964
236.2527-0.31860.59735.5331-0.04634.34310.5627-0.5160.619-0.2416-1.0179-2.14041.43521.46920.58720.69470.24310.0871.00130.08191.0992513.9824-6.1884284.4942
248.44812.02450.96837.1988-1.28826.9627-0.1215-1.0747-0.63980.199-0.0599-1.21010.91321.11330.14720.54580.26240.06660.6399-0.01340.4782502.2415-10.626294.0481
252.85370.0203-2.16893.68981.68175.2764-0.17680.4364-0.4472-0.8499-0.184100.59590.05360.18130.67410.1650.13720.33860.03410.4324498.275-3.9047273.958
266.2431-2.1009-1.62176.4126-0.44275.04760.08990.2652-0.3013-0.8299-0.11750.23580.09050.1377-0.1210.53710.05430.08590.29090.0270.3117493.39430.6477278.6667
275.4321-1.14060.10813.4922-3.31653.8242-0.1014-0.3373-0.561-0.2130.35640.57941.1152-0.217-0.15450.5778-0.00970.07590.304-0.0270.3371487.1931-9.1629295.0811
282.8901-0.7016-1.15096.1395-2.22747.33230.38310.0730.4237-0.4255-0.295-0.5941-0.42630.4989-0.08350.35730.02350.12050.2543-0.02520.3763496.56996.0514285.3013
295.16191.0888-2.84359.4017-4.27173.31240.5986-0.54070.60340.479-0.3904-0.4186-1.0841.3588-0.26110.5496-0.1269-0.00420.4835-0.08280.3863498.5167.9232292.8145
304.4798-0.6806-1.5177.5286-2.3498.01880.144-0.46240.12920.4809-0.0954-0.42310.16150.52520.05690.36870.03360.00030.3151-0.04940.255495.778-2.4657294.8967
312.5906-0.5072-1.04116.6487-2.64166.37140.0918-0.3174-0.247-0.3574-0.3043-0.51170.82270.61120.140.45140.1040.05370.32130.05040.3842496.0256-7.3531290.2215
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 105 )
2X-RAY DIFFRACTION2chain 'A' and (resid 106 through 149 )
3X-RAY DIFFRACTION3chain 'A' and (resid 150 through 208 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 17 )
5X-RAY DIFFRACTION5chain 'B' and (resid 18 through 52 )
6X-RAY DIFFRACTION6chain 'B' and (resid 53 through 73 )
7X-RAY DIFFRACTION7chain 'B' and (resid 74 through 107 )
8X-RAY DIFFRACTION8chain 'B' and (resid 108 through 155 )
9X-RAY DIFFRACTION9chain 'B' and (resid 156 through 185 )
10X-RAY DIFFRACTION10chain 'B' and (resid 186 through 223 )
11X-RAY DIFFRACTION11chain 'D' and (resid 57 through 71 )
12X-RAY DIFFRACTION12chain 'D' and (resid 72 through 89 )
13X-RAY DIFFRACTION13chain 'D' and (resid 90 through 122 )
14X-RAY DIFFRACTION14chain 'D' and (resid 123 through 146 )
15X-RAY DIFFRACTION15chain 'D' and (resid 147 through 262 )
16X-RAY DIFFRACTION16chain 'L' and (resid 1 through 105 )
17X-RAY DIFFRACTION17chain 'L' and (resid 106 through 208 )
18X-RAY DIFFRACTION18chain 'H' and (resid 1 through 107 )
19X-RAY DIFFRACTION19chain 'H' and (resid 108 through 129 )
20X-RAY DIFFRACTION20chain 'H' and (resid 130 through 223 )
21X-RAY DIFFRACTION21chain 'C' and (resid 57 through 71 )
22X-RAY DIFFRACTION22chain 'C' and (resid 72 through 89 )
23X-RAY DIFFRACTION23chain 'C' and (resid 90 through 99 )
24X-RAY DIFFRACTION24chain 'C' and (resid 100 through 126 )
25X-RAY DIFFRACTION25chain 'C' and (resid 127 through 146 )
26X-RAY DIFFRACTION26chain 'C' and (resid 147 through 163 )
27X-RAY DIFFRACTION27chain 'C' and (resid 164 through 174 )
28X-RAY DIFFRACTION28chain 'C' and (resid 175 through 206 )
29X-RAY DIFFRACTION29chain 'C' and (resid 207 through 228 )
30X-RAY DIFFRACTION30chain 'C' and (resid 229 through 247 )
31X-RAY DIFFRACTION31chain 'C' and (resid 248 through 262 )

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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