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- PDB-6q0i: Inferred intermediate I-7 (I-7-6) of the human antibody lineage 6... -

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Basic information

Entry
Database: PDB / ID: 6q0i
TitleInferred intermediate I-7 (I-7-6) of the human antibody lineage 652 in complex with influenza hemagglutinin head domain of A/Beijing/262/95(H1N1)
Components
  • Fab heavy chain
  • Fab lambda chain
  • Hemagglutinin
KeywordsIMMUNE SYSTEM / antibody
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
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
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.702 Å
AuthorsMcCarthy, K.R. / Harrison, S.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI089618 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI117892 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Affinity maturation in a human humoral response to influenza hemagglutinin.
Authors: McCarthy, K.R. / Raymond, D.D. / Do, K.T. / Schmidt, A.G. / Harrison, S.C.
History
DepositionAug 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
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 / _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
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
H: Fab heavy chain
L: Fab lambda chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4015
Polymers74,0873
Non-polymers3132
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: biolayer interferometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-27 kcal/mol
Surface area28510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.950, 70.410, 203.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hemagglutinin


Mass: 25425.271 Da / Num. of mol.: 1 / Fragment: Head domain, residues 65-280
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Beijing/262/1995(H1N1))
Strain: A/Beijing/262/1995(H1N1) / Gene: HA / Cell line (production host): BTI-Tn-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: B4UPF7
#2: Antibody Fab heavy chain


Mass: 25731.740 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293F / Production host: Homo sapiens (human)
#3: Antibody Fab lambda chain


Mass: 22930.193 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293F / Production host: Homo sapiens (human)
#4: 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
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
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: 2.52 Å3/Da / Density % sol: 51.16 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 100mM lithium sulfate, 30% (w/v) PEG 6000, 100mM CHES

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.702→48.881 Å / Num. obs: 21279 / % possible obs: 99.8 % / Redundancy: 8.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.07173 / Net I/σ(I): 24.15
Reflection shellResolution: 2.702→2.799 Å / Rmerge(I) obs: 1.038 / Num. unique obs: 18093 / CC1/2: 0.896 / % possible all: 99.23

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.702→48.881 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.65
RfactorNum. reflection% reflection
Rfree0.2554 1066 5.01 %
Rwork0.2134 --
obs0.2156 21260 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 172.16 Å2 / Biso mean: 76.07 Å2 / Biso min: 33.88 Å2
Refinement stepCycle: final / Resolution: 2.702→48.881 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4974 0 20 0 4994
Biso mean--95.35 --
Num. residues----650
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.702-2.82460.35131140.2937248099
2.8246-2.97350.32621200.27422460100
2.9735-3.15980.31621390.25472476100
3.1598-3.40370.30061310.24942510100
3.4037-3.74610.26811310.22932511100
3.7461-4.28790.25021360.19992522100
4.2879-5.40120.22311590.16932536100
5.4012-48.8810.23281360.20992699100
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)
10.5225-0.4813-0.00920.75140.02540.1439-0.1714-0.0270.69770.37270.3198-0.114-0.05410.57690.02430.8035-0.22450.01780.65470.01580.669111.716712.4491-127.6148
20.9579-1.38770.8436.7556-2.45651.3920.71990.41590.9141-2.5453-0.5065-0.88521.32411.09960.5430.3369-0.09640.19211.0743-00.689713.37945.7253-129.4531
30.32990.1045-0.10461.0309-0.06820.0077-0.33211.0428-0.5312-1.83260.27890.49710.55290.05780.01371.0876-0.12040.24850.8907-0.08040.73399.75982.0719-135.0491
40.5743-0.00641.5513-0.1413-0.39491.7908-0.258-0.30050.01280.67020.25960.191-0.5752-0.634900.6891-0.05210.03480.608-0.05680.63545.26125.8037-112.0001
51.3720.6559-0.34181.96370.26481.50480.0316-0.3487-0.07370.19880.21410.13630.27830.0381-00.5832-0.08640.05310.4984-0.04170.60234.0319-2.1702-115.5804
60.6203-0.15020.60780.9087-0.36070.27170.181-0.6313-0.72810.33120.298-0.25630.4401-0.710500.87610.03160.04150.5809-0.01560.723111.7568-11.2359-110.9412
70.01130.0679-0.1968-0.0284-0.06530.18360.28330.5398-0.22410.0723-0.7737-0.06020.28990.362401.1285-0.0829-0.0191.2754-0.00490.999124.6062-3.8585-111.7386
80.1307-0.2767-0.04030.8908-0.19150.20060.472-0.0814-1.2327-0.1647-0.1309-0.06071.26730.143300.7431-0.0899-0.00460.7166-0.08860.65585.7389-6.7026-122.6764
90.29450.20440.14980.2666-0.12930.26990.39760.01630.43040.37920.212-0.0507-0.20230.0360.00250.6207-0.04830.03610.6228-0.06690.57534.25450.1821-121.7255
100.6179-0.19470.81992.43940.47540.8567-0.0564-0.0827-0.1471-0.22480.210.23880.6392-0.18170.00030.48790.0779-0.02220.5694-0.01070.457411.9447-6.1767-77.9086
110.52880.9461-0.84391.1026-1.29941.19510.26860.1321-0.20620.66760.3175-0.84190.91110.415600.69630.13390.01970.5580.00340.57820.2826-3.4308-82.4953
120.67910.3157-0.80971.2462-0.29211.91-0.25680.2581-0.285-0.07990.0826-0.05110.3019-0.0446-00.46260.12390.00650.538-0.01030.585616.4202-3.6316-80.1048
130.58280.63460.10861.2127-0.18090.12830.64260.43240.2639-0.3014-0.6118-0.1745-1.3847-1.211-0.20270.84360.35790.0830.58670.06940.5067-6.094714.7787-48.2307
140.3304-0.7272-0.44310.61520.81171.1536-0.33970.17650.1564-0.1710.2058-0.1164-0.1612-0.0677-0.01080.60710.1272-0.0350.38270.12750.4623-0.35627.7323-58.2243
151.83820.19041.00061.3114-1.28742.4236-0.3996-0.1574-0.0590.51730.3452-0.02590.054-0.3172-0.00020.45040.0750.06150.40090.08990.4181-3.1095.8375-54.6682
161.6337-0.48780.19442.76150.03662.64780.01890.02190.1075-0.07230.2034-0.0805-0.210.1863-00.28420.08130.05220.4570.03670.435216.338216.8617-83.633
172.97060.1004-0.37494.37231.54541.9906-0.1015-0.1834-0.1140.0510.4712-0.2989-0.04570.199700.50980.12390.01830.4222-0.01880.47186.23717.8696-46.3849
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 51 through 76 )A51 - 76
2X-RAY DIFFRACTION2chain 'A' and (resid 77 through 101 )A77 - 101
3X-RAY DIFFRACTION3chain 'A' and (resid 102 through 115 )A102 - 115
4X-RAY DIFFRACTION4chain 'A' and (resid 116 through 146 )A116 - 146
5X-RAY DIFFRACTION5chain 'A' and (resid 147 through 184 )A147 - 184
6X-RAY DIFFRACTION6chain 'A' and (resid 185 through 213 )A185 - 213
7X-RAY DIFFRACTION7chain 'A' and (resid 214 through 228 )A214 - 228
8X-RAY DIFFRACTION8chain 'A' and (resid 229 through 247 )A229 - 247
9X-RAY DIFFRACTION9chain 'A' and (resid 248 through 263 )A248 - 263
10X-RAY DIFFRACTION10chain 'H' and (resid 1 through 41 )H1 - 41
11X-RAY DIFFRACTION11chain 'H' and (resid 42 through 60 )H42 - 60
12X-RAY DIFFRACTION12chain 'H' and (resid 61 through 136 )H61 - 136
13X-RAY DIFFRACTION13chain 'H' and (resid 137 through 151 )H137 - 151
14X-RAY DIFFRACTION14chain 'H' and (resid 152 through 184 )H152 - 184
15X-RAY DIFFRACTION15chain 'H' and (resid 185 through 231 )H185 - 231
16X-RAY DIFFRACTION16chain 'L' and (resid 2 through 116 )L2 - 116
17X-RAY DIFFRACTION17chain 'L' and (resid 117 through 213 )L117 - 213

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