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- PDB-6q0h: Inferred intermediate I-7 (I-7-0) of the human antibody lineage 6... -

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Basic information

Entry
Database: PDB / ID: 6q0h
TitleInferred intermediate I-7 (I-7-0) 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: 2.75 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)74,9227
Polymers74,0003
Non-polymers9224
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: biolayer interferometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7310 Å2
ΔGint-21 kcal/mol
Surface area28690 Å2
Unit cell
Length a, b, c (Å)52.810, 70.580, 200.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 2 molecules HL

#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)

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Hemagglutinin


Mass: 25338.191 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 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): BTI-Tn-5B1-4 / References: UniProt: B4UPF7
#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

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Non-polymers , 3 types, 3 molecules

#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3

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Details

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: 2.53 Å3/Da / Density % sol: 51.39 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 5% (v/v) PEG 400, 1.1M sodium citrate

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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: 2.75→48.585 Å / Num. obs: 20295 / % possible obs: 99.95 % / Redundancy: 8.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06853 / Net I/σ(I): 23.15
Reflection shellResolution: 2.75→2.848 Å / Redundancy: 9 % / Rmerge(I) obs: 0.9509 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1980 / CC1/2: 0.78 / % possible all: 100

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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: 2.75→48.585 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.33
RfactorNum. reflection% reflection
Rfree0.2692 981 4.83 %
Rwork0.2413 --
obs0.2426 20291 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 292.57 Å2 / Biso mean: 73.95 Å2 / Biso min: 41.81 Å2
Refinement stepCycle: final / Resolution: 2.75→48.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4996 0 137 0 5133
Biso mean--117.68 --
Num. residues----653
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.7502-2.89510.28461220.33792702
2.8951-3.07650.31171420.29612716
3.0765-3.3140.31921340.28282708
3.314-3.64740.26111270.27282750
3.6474-4.17490.29831600.23772726
4.1749-5.2590.23321370.19792790
5.259-48.5850.26291590.23342918
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)
12.1474-1.47320.15061.49691.64642.41160.2669-1.15080.57051.0486-0.30380.63880.109-0.47560.00210.8074-0.10550.06770.8216-0.04880.8092-13.597712.3291126.8848
24.89041.89832.54681.73520.2952.03150.04250.34530.0244-0.15620.3393-0.4012-0.2352-0.08330.00020.64310.0392-0.01060.81970.06140.6481-4.51596.9361114.5503
34.94192.00443.18041.25262.1092.84070.6940.2836-0.81730.60510.0881-0.38350.8457-0.07140.00630.7646-0.0322-0.13470.6170.12760.7842-9.9236-3.3208117.1467
41.2806-0.17891.62380.546-1.11592.72220.415-0.0364-0.5011-0.08610.0779-0.52052.64740.65740.13020.55740.26910.21250.9007-0.04450.672-10.7556-8.812171.7423
55.78212.54073.16791.10321.37394.1589-0.0670.862-1.66860.42470.81940.08330.58472.09730.42311.05350.20310.03340.75470.31620.9564-7.2887-10.050682.9124
63.46350.7977-0.87781.93611.63521.82970.1619-1.0035-0.49540.1266-0.07550.14121.4259-0.3979-0.00020.7752-0.09750.00190.77670.05190.6416-18.699-4.739981.6684
71.34330.216-0.69821.4221.72172.31380.1269-0.2829-0.43410.7648-0.3401-0.2951.4298-0.4424-0.00010.845-0.1660.01430.60310.09810.6594-15.8159-9.670877.393
80.2729-0.3546-0.49990.96830.19210.33060.0088-0.31030.34340.28820.2183-0.46361.0474-0.12110.00060.4313-0.0975-0.05550.86280.10160.5867-14.61431.753393.1945
91.5144-0.3945-0.16851.0091-0.19371.5865-0.19770.2536-0.09250.27660.257-0.4681-0.1504-0.12170.00030.6188-0.0941-0.01150.4063-0.03980.5099-1.52853.071554.3057
102.81330.0661-1.39374.0207-0.21073.1087-0.0256-0.089-0.00840.40740.0871-0.225-0.13060.03400.4986-0.04340.01940.311-0.02730.39353.21544.569555.0524
111.91340.3542-0.60333.8956-0.92132.95490.0475-0.4920.01580.1526-0.05610.1022-0.0289-0.13490.00010.4106-0.02510.05910.72310.00440.4508-16.579714.490184.3358
120.39640.2351-0.67890.31530.90851.27870.1328-0.01150.2454-0.20350.1704-0.06250.1117-0.4417-0.00010.66270.09660.04910.53390.04720.5562-7.324313.619157.2297
131.8776-0.5077-0.70414.7875-0.55511.5040.16350.0863-0.0235-0.1396-0.02790.3479-0.0911-0.013400.5222-0.05060.09770.40010.02840.6092-7.593617.052346.6662
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 53 through 110 )A53 - 110
2X-RAY DIFFRACTION2chain 'A' and (resid 111 through 146 )A111 - 146
3X-RAY DIFFRACTION3chain 'A' and (resid 147 through 263 )A147 - 263
4X-RAY DIFFRACTION4chain 'H' and (resid 1 through 17 )H1 - 17
5X-RAY DIFFRACTION5chain 'H' and (resid 18 through 32 )H18 - 32
6X-RAY DIFFRACTION6chain 'H' and (resid 33 through 64 )H33 - 64
7X-RAY DIFFRACTION7chain 'H' and (resid 65 through 100 )H65 - 100
8X-RAY DIFFRACTION8chain 'H' and (resid 101 through 123 )H101 - 123
9X-RAY DIFFRACTION9chain 'H' and (resid 124 through 174 )H124 - 174
10X-RAY DIFFRACTION10chain 'H' and (resid 175 through 232 )H175 - 232
11X-RAY DIFFRACTION11chain 'L' and (resid 2 through 97 )L2 - 97
12X-RAY DIFFRACTION12chain 'L' and (resid 98 through 132 )L98 - 132
13X-RAY DIFFRACTION13chain 'L' and (resid 133 through 213 )L133 - 213

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