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- PDB-4xrc: Antibody hemagglutinin Complexes -

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Basic information

Entry
Database: PDB / ID: 4xrc
TitleAntibody hemagglutinin Complexes
Components
  • H5.3 Fab heavy chain
  • H5.3 Fab light chain
  • Hemagglutinin
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Antibody / hemagglutinin / neutralization / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


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 / 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 / Resolution: 2.74 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)5R21 AI092268 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272200900047C 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 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Aug 12, 2015Group: Database references
Revision 1.3Sep 9, 2015Group: Source and taxonomy
Revision 1.4Feb 24, 2016Group: Data collection
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 / Category: chem_comp / 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 Fab light chain
B: H5.3 Fab heavy chain
D: Hemagglutinin
L: H5.3 Fab light chain
H: H5.3 Fab heavy chain
C: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,7677
Polymers141,1966
Non-polymers5711
Water1,892105
1
A: H5.3 Fab light chain
B: H5.3 Fab heavy chain
D: Hemagglutinin


Theoretical massNumber of molelcules
Total (without water)70,5983
Polymers70,5983
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
L: H5.3 Fab light chain
H: H5.3 Fab heavy chain
C: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1694
Polymers70,5983
Non-polymers5711
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)248.420, 51.080, 127.610
Angle α, β, γ (deg.)90.00, 99.94, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody H5.3 Fab 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 Fab 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 Hemagglutinin /


Mass: 24305.580 Da / Num. of mol.: 2 / Fragment: UNP residues 15-226
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Vietnam/1203/2004(H5N1) / Gene: HA / Production host: Escherichia coli (E. coli) / References: UniProt: Q6Q9G9, 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.: 105 / 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: 57.35 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 200 mM ammonium sulfate, 100 mM HEPES pH 7.5, 25% PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.74→50 Å / Num. obs: 42101 / % possible obs: 99.8 % / Redundancy: 5.1 % / Rsym value: 0.085 / Net I/σ(I): 14.5
Reflection shellResolution: 2.74→2.81 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 2.2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIXdev_1760refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.74→41.918 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 27.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2478 2000 4.75 %
Rwork0.1918 --
obs0.1945 42101 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.74→41.918 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9740 0 38 105 9883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410052
X-RAY DIFFRACTIONf_angle_d0.90713713
X-RAY DIFFRACTIONf_dihedral_angle_d11.9263580
X-RAY DIFFRACTIONf_chiral_restr0.0371550
X-RAY DIFFRACTIONf_plane_restr0.0041738
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.74-2.80850.33791420.28192847X-RAY DIFFRACTION100
2.8085-2.88440.35021400.27372806X-RAY DIFFRACTION100
2.8844-2.96930.29341420.26052865X-RAY DIFFRACTION100
2.9693-3.06510.31471400.26322799X-RAY DIFFRACTION100
3.0651-3.17460.31251420.24672860X-RAY DIFFRACTION100
3.1746-3.30170.30611410.24272818X-RAY DIFFRACTION100
3.3017-3.45190.31721430.23352866X-RAY DIFFRACTION100
3.4519-3.63380.26151430.21352857X-RAY DIFFRACTION100
3.6338-3.86130.25921410.19222833X-RAY DIFFRACTION100
3.8613-4.15920.23141440.16912880X-RAY DIFFRACTION100
4.1592-4.57730.17791420.14442874X-RAY DIFFRACTION100
4.5773-5.23850.19571450.1412898X-RAY DIFFRACTION100
5.2385-6.59580.25671460.16762918X-RAY DIFFRACTION100
6.5958-41.9230.20771490.17462980X-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)
10.4574-0.1914-0.52973.11342.89313.022-0.05410.11670.24410.55680.106-0.0312-0.3042-2.54280.66331.06430.33780.18921.6947-0.0450.5803450.991838.1374294.5851
22.8846-0.09690.58121.9520.60544.4746-0.3311-0.6732-0.13820.19630.0681-0.1202-0.5631-2.54120.30370.94190.47880.25111.1489-0.17250.4087459.853138.8753297.5412
33.31480.07481.3270.6275-1.41823.6282-0.6614-1.24790.13690.35230.64320.4037-0.6136-0.75970.2040.76470.54690.13891.40270.11980.5207443.808241.1542272.4897
41.4375-0.0877-2.5820.04060.06116.9734-0.663-0.8964-0.96990.60430.32940.28861.1965-1.4690.52670.89010.28570.24791.48390.3860.7004439.929232.952268.6857
55.74222.45354.18554.15133.22644.0335-0.25220.1821-0.27-0.32590.0622-0.2075-0.50610.21850.24780.65110.07030.11890.3391-0.00470.3155478.30338.7231281.0762
62.3384-1.52031.41342.2697-0.31443.4606-0.20960.1284-0.42370.11790.06770.18620.0619-0.31510.12120.69730.0570.17270.3547-0.04070.384474.133731.2079284.686
72.6245-0.34083.64940.8741-1.82146.206-0.5366-0.21430.11990.3020.48480.2261-0.5823-0.49190.0960.72250.17610.09760.6662-0.06970.3912455.637645.482267.4797
86.33562.1589-1.40256.18410.82995.7048-0.35820.19441.45070.13130.34510.8923-1.5137-0.97380.01940.94350.2802-0.03050.794-0.00070.5232445.69752.7687259.4904
95.5918-4.896-1.26017.37695.53136.34530.43750.16430.8512-0.198-0.0251-1.15810.84021.7832-0.35560.85320.06560.13570.99410.03940.5508495.247714.3705310.5292
102.4499-3.20810.92394.2815-0.53954.8253-0.1491-0.12951.2360.2596-0.165-1.3622-1.17161.07230.1690.9574-0.31920.16570.7216-0.05420.9225491.158925.7601314.0595
117.4506-2.8170.74994.8833-0.80625.52460.0206-0.5979-0.07220.2583-0.066-0.14690.3670.18870.0390.9516-0.11940.19120.61090.02760.2612483.806211.9521316.5631
124.4398-1.8099-1.22183.3459-1.00947.30250.1515-0.36750.09130.2380.17480.1256-0.008-0.6208-0.2960.7318-0.03650.13220.5948-0.04710.3051475.336916.6019317.715
132.1074-1.06971.55560.4569-1.49485.8996-0.365-0.25650.1531-0.0601-0.0321-0.1849-0.7771-0.23080.31850.65310.00210.10640.2361-0.02590.4954494.345825.5959252.2649
143.86210.33541.32896.062.8817.150.0228-0.10830.03550.6859-0.2140.45280.4937-0.91330.15180.8362-0.06730.24050.5894-0.04840.4221481.150822.102228.2089
152.9478-2.1678-0.21616.25450.3395.36490.120.1447-0.1013-1.11720.0326-0.18990.47490.7026-0.22420.68830.06730.17660.3329-0.01550.4672504.63676.2739250.2571
162.4053-1.47422.00353.3054-1.26477.72130.1663-0.24880.32380.08520.0333-0.28140.40750.4907-0.2450.81780.09750.18470.6735-0.07490.4404492.225219.043217.1226
175.9192-2.6756-2.42898.41743.54156.79210.19730.39280.4231-0.3150.3262-0.6608-0.45960.3594-0.480.8355-0.04260.23660.6678-0.10880.48491.14924.6806214.1717
188.68892.85371.62456.86910.06570.32411.5511.4239-0.65660.229-0.5486-1.17411.1341.03291.49551.18620.75860.01361.08530.36420.5187506.741-5.5506288.1758
192.3131-1.85890.45794.3496-0.52580.81240.0376-0.405-0.48970.62560.13190.47421.20870.5039-0.43031.73180.78180.09840.95230.12260.8276503.6763-6.8708285.8353
200.38111.5101-0.86989.27110.00325.44420.0193-0.0044-0.37051.5681-0.9307-1.23951.40822.23110.25130.53160.43720.33381.54880.22430.8483510.72621.8182286.2633
213.14451.7513-1.57281.67850.08454.2902-0.2018-0.6648-0.29710.0621-0.1832-0.48011.04510.63260.29410.63280.25460.11410.59020.04450.5062497.56672.3382286.4003
222.41940.0883-2.07045.0793-0.74446.60020.2174-0.03190.2554-0.4393-0.1382-0.05320.20750.2211-0.05260.36790.07910.07260.35850.00490.267490.661911.7299284.5832
236.90036.7242-6.75426.535-6.57656.7660.9183-0.56530.56621.514-0.55440.3789-1.66690.4856-0.31720.5938-0.0029-0.00310.4291-0.04950.2901490.304414.1722297.9833
242.56030.7069-1.22855.9422-1.34086.14320.2314-0.36170.07380.3651-0.2205-0.5690.01520.84180.0270.50530.08210.02420.44950.02770.2729496.25489.7265289.7105
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 15 )
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 105 )
3X-RAY DIFFRACTION3chain 'A' and (resid 106 through 172 )
4X-RAY DIFFRACTION4chain 'A' and (resid 173 through 208 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 33 )
6X-RAY DIFFRACTION6chain 'B' and (resid 34 through 107 )
7X-RAY DIFFRACTION7chain 'B' and (resid 108 through 185 )
8X-RAY DIFFRACTION8chain 'B' and (resid 186 through 223 )
9X-RAY DIFFRACTION9chain 'D' and (resid 57 through 89 )
10X-RAY DIFFRACTION10chain 'D' and (resid 90 through 99 )
11X-RAY DIFFRACTION11chain 'D' and (resid 100 through 135 )
12X-RAY DIFFRACTION12chain 'D' and (resid 136 through 262 )
13X-RAY DIFFRACTION13chain 'L' and (resid 1 through 120 )
14X-RAY DIFFRACTION14chain 'L' and (resid 121 through 208 )
15X-RAY DIFFRACTION15chain 'H' and (resid 1 through 119 )
16X-RAY DIFFRACTION16chain 'H' and (resid 120 through 167 )
17X-RAY DIFFRACTION17chain 'H' and (resid 168 through 223 )
18X-RAY DIFFRACTION18chain 'C' and (resid 57 through 71 )
19X-RAY DIFFRACTION19chain 'C' and (resid 72 through 86 )
20X-RAY DIFFRACTION20chain 'C' and (resid 87 through 99 )
21X-RAY DIFFRACTION21chain 'C' and (resid 100 through 146 )
22X-RAY DIFFRACTION22chain 'C' and (resid 147 through 201 )
23X-RAY DIFFRACTION23chain 'C' and (resid 202 through 213 )
24X-RAY DIFFRACTION24chain 'C' and (resid 214 through 262 )

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