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- PDB-6wiz: Crystal structure of Fab 54-1G05 bound to H1 influenza hemagglutinin -

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Basic information

Entry
Database: PDB / ID: 6wiz
TitleCrystal structure of Fab 54-1G05 bound to H1 influenza hemagglutinin
Components
  • Fab 54-1G05 heavy chain
  • Fab 54-1G05 light chain
  • Hemagglutinin HA1
  • Hemagglutinin HA2
KeywordsIMMUNE SYSTEM / Antibody / Influenza hemagglutinin
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
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å
AuthorsWu, N.C. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56 AI127371 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)K99 AI139445 United States
CitationJournal: Cell Host Microbe / Year: 2020
Title: Convergent Evolution in Breadth of Two VH6-1-Encoded Influenza Antibody Clonotypes from a Single Donor.
Authors: Wu, N.C. / Andrews, S.F. / Raab, J.E. / O'Connell, S. / Schramm, C.A. / Ding, X. / Chambers, M.J. / Leung, K. / Wang, L. / Zhang, Y. / Mascola, J.R. / Douek, D.C. / Ledgerwood, J.E. / ...Authors: Wu, N.C. / Andrews, S.F. / Raab, J.E. / O'Connell, S. / Schramm, C.A. / Ding, X. / Chambers, M.J. / Leung, K. / Wang, L. / Zhang, Y. / Mascola, J.R. / Douek, D.C. / Ledgerwood, J.E. / McDermott, A.B. / Wilson, I.A.
History
DepositionApr 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jul 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 / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 23, 2020Group: Database references / Structure summary / Category: chem_comp / citation
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first
Revision 1.4Oct 18, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemagglutinin HA1
B: Hemagglutinin HA2
H: Fab 54-1G05 heavy chain
L: Fab 54-1G05 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,9725
Polymers104,7514
Non-polymers2211
Water00
1
A: Hemagglutinin HA1
B: Hemagglutinin HA2
H: Fab 54-1G05 heavy chain
L: Fab 54-1G05 light chain
hetero molecules

A: Hemagglutinin HA1
B: Hemagglutinin HA2
H: Fab 54-1G05 heavy chain
L: Fab 54-1G05 light chain
hetero molecules

A: Hemagglutinin HA1
B: Hemagglutinin HA2
H: Fab 54-1G05 heavy chain
L: Fab 54-1G05 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,91715
Polymers314,25312
Non-polymers6643
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Unit cell
Length a, b, c (Å)187.378, 187.378, 132.533
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Hemagglutinin HA1


Mass: 36480.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A7Y8I1*PLUS
#2: Protein Hemagglutinin HA2


Mass: 19956.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A7UPX0*PLUS
#3: Antibody Fab 54-1G05 heavy chain


Mass: 24651.646 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#4: Antibody Fab 54-1G05 light chain


Mass: 23662.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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
Has ligand of interestN
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: 6.41 Å3/Da / Density % sol: 80.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 50% PEG 200 and 0.1 M CHES pH 9.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 4.2→46.844 Å / Num. obs: 19952 / % possible obs: 99.9 % / Redundancy: 19.2 % / Biso Wilson estimate: 111.32 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.401 / Rpim(I) all: 0.093 / Rrim(I) all: 0.412 / Net I/σ(I): 4.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
4.2-4.619.10.998961147030.970.2321.0172.6100
10.29-46.8418.60.142682614420.9960.0330.1439.899

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Aimless0.7.2data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FYT

6fyt


Resolution: 4.2→46.844 Å / SU ML: 0.75 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 43.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3892 923 4.67 %
Rwork0.3226 18837 -
obs0.3258 19760 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 289.24 Å2 / Biso mean: 134.9033 Å2 / Biso min: 50.01 Å2
Refinement stepCycle: final / Resolution: 4.2→46.844 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7288 0 14 0 7302
Biso mean--114.35 --
Num. residues----937
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
4.2001-4.42140.35551340.3354264199
4.4214-4.69820.36511200.3071265598
4.6982-5.06050.3931150.3126267699
5.0605-5.56910.4051270.31642692100
5.5691-6.37320.46561390.3591269999
6.3732-8.0230.40981430.3813268699
8.023-46.8440.35621450.2868278898
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)
11.2368-0.278-1.00222.1274-1.45594.1901-0.1669-0.33060.28670.3441-0.0491-0.0301-1.2911.00010.29431.4217-0.14690.06661.1454-0.09610.679396.256-31.1911.191
23.66181.8309-1.27683.12132.38046.3070.5282-1.28061.21941.0590.16960.0667-1.21820.1154-0.66851.9370.13340.31651.2821-0.23320.990488.139-32.75250.343
35.06921.44172.3823-0.4452-2.10913.23070.31870.2011-0.39360.52840.3646-0.0571-0.22540.3184-0.63581.46810.03360.25551.244-0.42041.034188.489-39.86149.113
42.87790.73640.03991.85550.09058.048-0.7107-0.02070.8431-0.4733-0.58140.9589-0.5116-0.3241.24881.053-0.0869-0.03050.6918-0.07941.174496.214-34.9067.416
52.5642.0806-2.03526.5814-5.65444.68690.30670.35690.1873-0.9578-0.2122-0.251-0.66420.2934-0.12361.29830.14620.03261.0280.00350.456592.639-36.927-22.915
61.7952-0.422-0.71733.1506-2.6614.5609-0.29990.14350.3608-0.516-0.1639-0.2082-0.1517-0.19330.24850.8367-0.08260.03830.9845-0.05020.310395.383-44.766-13.017
71.64050.06771.33427.74850.70832.2814-0.47492.57281.5386-0.97162.29070.2756-0.9184-0.4466-1.49882.08250.12530.4413.0370.04971.064488.529-40.84-51.336
82.8049-0.0817-0.20075.15481.88392.86091.0060.10990.883-0.4531-0.382-0.3368-0.5658-0.2739-0.56781.5287-0.04190.1151.15620.22910.71492.841-10.604-26.794
93.45281.99231.9889.4527-3.09855.9033-0.5370.53240.9604-0.66540.32522.30640.2485-0.05030.39430.9725-0.0438-0.14691.02530.23551.274972.00816.925-22.749
105.0841-0.6821-0.2538.79562.83853.04810.87950.06270.23360.5298-0.45510.9785-0.7076-0.4594-0.34951.43660.00110.23611.07210.16260.849975.305-17.975-15.635
111.17010.35990.54823.4397-0.20631.5163-0.10340.5654-0.1985-0.24350.39972.32370.0716-0.8593-0.13520.9078-0.20470.01882.04910.00012.009256.06713.044-22.148
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 10:97 )A10 - 97
2X-RAY DIFFRACTION2( CHAIN A AND RESID 98:198 )A98 - 198
3X-RAY DIFFRACTION3( CHAIN A AND RESID 199:264 )A199 - 264
4X-RAY DIFFRACTION4( CHAIN A AND RESID 265:324 )A265 - 324
5X-RAY DIFFRACTION5( CHAIN B AND RESID 1:62 )B1 - 62
6X-RAY DIFFRACTION6( CHAIN B AND RESID 63:152 )B63 - 152
7X-RAY DIFFRACTION7( CHAIN B AND RESID 153:173 )B153 - 173
8X-RAY DIFFRACTION8( CHAIN H AND RESID 1:107 )H1 - 107
9X-RAY DIFFRACTION9( CHAIN H AND RESID 108:213 )H108 - 213
10X-RAY DIFFRACTION10( CHAIN L AND RESID 1:108 )L1 - 108
11X-RAY DIFFRACTION11( CHAIN L AND RESID 109:213 )L109 - 213

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