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- PDB-4xnm: Antibody Influenza H5 Complex -

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Basic information

Entry
Database: PDB / ID: 4xnm
TitleAntibody Influenza H5 Complex
Components
  • H5.3 FAB Heavy Chain
  • H5.3 FAB Light Chain
  • Hemagglutinin
KeywordsViral protein/Immune system / Antibody / Influenza / 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 / Resolution: 2.51 Å
AuthorsWinarski, K.L. / Spiler, B.W.
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)AI092268 United States
Citation
Journal: 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.
#1: Journal: To Be Published
Title: Antibody Influenza H5 Complex
Authors: Winarski, K.L. / 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 / 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
L: H5.3 FAB Light Chain
H: H5.3 FAB Heavy Chain
A: H5.3 FAB Light Chain
B: H5.3 FAB Heavy Chain
C: Hemagglutinin
D: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,8637
Polymers145,2936
Non-polymers5711
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13070 Å2
ΔGint-54 kcal/mol
Surface area54200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)250.939, 51.427, 127.181
Angle α, β, γ (deg.)90.00, 99.83, 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: 26353.771 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) / Gene: HA / 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


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.78 Å3/Da / Density % sol: 55.8 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% PEG 10,000

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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: Oct 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.51→50 Å / Num. all: 53874 / Num. obs: 53874 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Redundancy: 4.9 % / Rsym value: 0.109 / Net I/σ(I): 14.2
Reflection shellResolution: 2.51→2.59 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.7 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1760)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.51→29.464 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2412 1999 3.71 %Random
Rwork0.2138 ---
obs0.2149 53874 96.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.51→29.464 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9648 0 38 83 9769
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029957
X-RAY DIFFRACTIONf_angle_d0.65913585
X-RAY DIFFRACTIONf_dihedral_angle_d11.7193543
X-RAY DIFFRACTIONf_chiral_restr0.0271537
X-RAY DIFFRACTIONf_plane_restr0.0041724
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.57030.32491240.34873221X-RAY DIFFRACTION84
2.5703-2.63970.34531370.35013547X-RAY DIFFRACTION94
2.6397-2.71730.381400.32663631X-RAY DIFFRACTION96
2.7173-2.8050.28371380.30583584X-RAY DIFFRACTION95
2.805-2.90520.31761420.28723666X-RAY DIFFRACTION96
2.9052-3.02140.28621420.28053691X-RAY DIFFRACTION97
3.0214-3.15870.31721420.2823686X-RAY DIFFRACTION98
3.1587-3.3250.31081420.27043704X-RAY DIFFRACTION98
3.325-3.5330.31311460.25033791X-RAY DIFFRACTION99
3.533-3.80530.25211470.22143812X-RAY DIFFRACTION100
3.8053-4.18730.21141480.20323839X-RAY DIFFRACTION100
4.1873-4.7910.18051480.16083825X-RAY DIFFRACTION100
4.791-6.02760.21811490.16893887X-RAY DIFFRACTION100
6.0276-29.46570.19781540.17623991X-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)
10.8319-0.3793-0.05720.1492-0.17412.03950.2146-0.20790.182-0.289-0.31390.2321-0.753-0.4026-0.05940.9434-0.00970.11250.5517-0.01760.7861267.231724.4251125.2502
23.8479-1.15230.62925.3316-2.02438.1925-0.238-0.10120.1499-0.6268-0.128-0.4765-0.34370.3630.38680.7368-0.02440.17870.3615-0.02690.6905273.890920.1202130.0726
35.25933.01283.65977.76744.56816.6087-0.0182-0.22770.09770.5977-0.04870.30610.0377-0.41460.04221.13280.08370.21430.5936-0.00050.5431258.415819.2577102.3076
43.4938-0.58890.95454.9580.02376.55310.140.20080.007-1.19080.1245-0.30760.61330.7117-0.28841.01790.07650.26170.4632-0.0540.7837281.6332-0.0459122.7785
51.6296-1.04552.2665-0.008-1.17937.46850.01610.29310.0564-0.3825-0.2402-0.06920.78710.45810.17691.1514-0.06310.22930.5017-0.03340.7262274.39811.1111.761
69.1002-4.5703-4.7678.66324.46245.90860.1335-0.5720.7738-0.13210.8174-0.7746-0.2870.838-0.87021.091-0.12270.18240.8901-0.21710.6724269.501319.746488.904
71.2638-0.5248-0.34456.13752.34892.4627-0.6053-0.12540.28910.86270.62910.57370.0075-1.37460.04351.0130.13790.20851.3261-0.16130.9003227.696234.0975169.0366
84.8189-0.77640.41050.2375-0.65655.2456-0.4456-0.51780.03610.56450.24480.1997-0.6888-1.44140.22051.02150.18330.22570.9171-0.13860.673236.800734.4961171.3513
91.60521.8654-0.96672.75470.78696.2145-0.1777-0.33931.21750.19161.2891-0.5591-0.9512-1.3535-0.74661.13310.70.11391.7223-0.02810.9022214.91642.1963152.698
104.89210.27241.62574.88062.19066.8075-0.1763-0.62750.17730.3010.23970.1536-0.3211-0.44490.01760.79270.28410.12931.010.1550.6445221.248935.406144.9591
115.5914-1.04610.83229.36633.97942.6183-0.3393-0.7897-0.46710.35740.28340.69980.8758-1.27850.17550.88060.1030.17221.10180.26620.7409216.073128.6214142.4323
122.0635-0.36490.56521.6352-0.61793.834-0.0550.1676-0.3659-0.015-0.044-0.00260.147-0.13990.08140.87060.01160.21470.5638-0.08590.6684252.197729.2349157.5318
136.892-0.88896.22790.557-1.68758.2415-0.1110.08750.2090.17950.19560.0922-0.2769-0.1874-0.06870.9070.06080.17010.5802-0.05160.6019233.988138.2518143.1149
145.5593-2.61692.55568.1541-1.85286.9786-0.4316-0.57080.66480.14660.69670.3504-0.7814-0.4506-0.25730.85840.06780.14080.7782-0.08030.7107225.038146.9476135.8601
158.9169-1.31391.94625.905-0.59436.85160.0342-0.205-0.66210.1672-0.1251-1.23421.59951.90240.09140.93750.31520.09251.13270.10370.9272281.9669-4.8866163.9957
165.99782.2793-5.00530.8626-1.34568.0505-0.58520.32630.1376-0.02320.1747-0.17571.1887-0.33210.47620.79630.00940.13840.5246-0.03830.7729269.61341.2466149.9018
173.71060.6189-2.40584.9121-2.01228.19270.2241-0.33350.17480.1839-0.1386-0.3204-0.10030.3846-0.09680.5460.01060.04180.4661-0.0480.5052269.85216.9706161.7472
186.5628-6.2892-6.85255.93276.56797.1942-0.19640.86411.3311-0.4280.5032-1.29850.15950.7523-0.18691.0638-0.23850.05671.18830.0060.7862272.339611.7268185.6352
195.0437-2.9556-1.17555.48115.80789.45490.2943-1.06940.83130.84360.1919-0.93340.81951.9045-0.50811.1681-0.1498-0.03351.39020.0850.938272.70169.4037182.9509
208.2449-7.065-0.43038.0899-2.37335.6274-0.0123-2.27191.25811.31230.3752-1.5801-0.76540.3754-0.29671.4088-0.3821-0.14411.2942-0.21750.78267.378217.5917193.6879
214.8924-2.3199-1.42217.4859-3.10373.79350.2561-0.2135-0.10310.1844-0.20460.11470.27090.4705-0.04391.0505-0.14930.08450.8638-0.16730.4561257.94669.0295183.4378
224.8265-1.9494-1.17732.8293-0.98245.60650.2329-0.56870.23970.5480.14210.1287-0.42240.0333-0.39430.9759-0.12390.14420.6645-0.06480.4612251.955512.1442192.7606
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 1 through 16 )
2X-RAY DIFFRACTION2chain 'L' and (resid 17 through 105 )
3X-RAY DIFFRACTION3chain 'L' and (resid 106 through 208 )
4X-RAY DIFFRACTION4chain 'H' and (resid 1 through 91 )
5X-RAY DIFFRACTION5chain 'H' and (resid 92 through 153 )
6X-RAY DIFFRACTION6chain 'H' and (resid 154 through 223 )
7X-RAY DIFFRACTION7chain 'A' and (resid 1 through 16 )
8X-RAY DIFFRACTION8chain 'A' and (resid 17 through 105 )
9X-RAY DIFFRACTION9chain 'A' and (resid 106 through 117 )
10X-RAY DIFFRACTION10chain 'A' and (resid 118 through 172 )
11X-RAY DIFFRACTION11chain 'A' and (resid 173 through 208 )
12X-RAY DIFFRACTION12chain 'B' and (resid 1 through 107 )
13X-RAY DIFFRACTION13chain 'B' and (resid 108 through 155 )
14X-RAY DIFFRACTION14chain 'B' and (resid 156 through 223 )
15X-RAY DIFFRACTION15chain 'C' and (resid 58 through 122 )
16X-RAY DIFFRACTION16chain 'C' and (resid 123 through 146 )
17X-RAY DIFFRACTION17chain 'C' and (resid 147 through 262 )
18X-RAY DIFFRACTION18chain 'D' and (resid 57 through 71 )
19X-RAY DIFFRACTION19chain 'D' and (resid 72 through 90 )
20X-RAY DIFFRACTION20chain 'D' and (resid 91 through 111 )
21X-RAY DIFFRACTION21chain 'D' and (resid 112 through 146 )
22X-RAY DIFFRACTION22chain 'D' and (resid 147 through 261 )

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