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- PDB-6q0e: Inferred precursor (UCA) of the human antibody lineage 652 in com... -

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Basic information

Entry
Database: PDB / ID: 6q0e
TitleInferred precursor (UCA) 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 light 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: 2.15 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 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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
L: Fab lambda light chain
H: Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9366
Polymers74,2343
Non-polymers7023
Water6,071337
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: biolayer interferometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-22 kcal/mol
Surface area28060 Å2
Unit cell
Length a, b, c (Å)52.030, 69.780, 200.700
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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Protein , 1 types, 1 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 / Cell line (production host): BTI-Tn-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: B4UPF7

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Antibody , 2 types, 2 molecules LH

#2: Antibody Fab lambda light chain


Mass: 22960.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Igl / Cell line (production host): 293F / Production host: Homo sapiens (human)
#3: Antibody Fab heavy chain


Mass: 25935.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IgH / Cell line (production host): 293F / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 340 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O

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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: 2.45 Å3/Da / Density % sol: 49.88 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM sodium chloride, 30% (v/v) PEG 400, 100 mM MES

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Data collection

DiffractionMean temperature: 291.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.15→48.292 Å / Num. obs: 40694 / % possible obs: 99.45 % / Redundancy: 7.05 % / Biso Wilson estimate: 28.93 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1408 / Net I/σ(I): 13.21
Reflection shellResolution: 2.15→2.227 Å / Num. unique obs: 4005 / CC1/2: 0.801 / % possible all: 99.78

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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: 2.15→48.292 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.08
RfactorNum. reflection% reflection
Rfree0.2485 2046 5.05 %
Rwork0.2303 --
obs0.2312 40536 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.88 Å2 / Biso mean: 39.5336 Å2 / Biso min: 18.18 Å2
Refinement stepCycle: final / Resolution: 2.15→48.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4987 0 105 337 5429
Biso mean--41.44 37.51 -
Num. residues----651
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.15-2.20.35141400.30422528100
2.2-2.2550.44851340.4124244696
2.255-2.31590.29211300.3235245298
2.3159-2.38410.31071490.27482531100
2.3841-2.4610.29831360.26952548100
2.461-2.5490.30141320.26212540100
2.549-2.6510.29031420.25752541100
2.651-2.77170.30871370.27452549100
2.7717-2.91780.27121330.25222604100
2.9178-3.10060.23881230.23362554100
3.1006-3.33990.24251500.22162566100
3.3399-3.67590.24161280.22042583100
3.6759-4.20760.20241310.18842602100
4.2076-5.30.1771500.15982642100
5.3-48.290.21661310.2122804100
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)
10.5692-0.3275-0.14970.2659-0.20.49210.2079-0.009-0.28080.1571-0.0094-0.04170.13370.2061-00.30350.038-0.11350.2841-0.06150.3246-14.0897-13.5984127.3627
20.3240.3785-0.05550.2322-0.0570.327-0.09460.1812-0.1014-0.18220.19430.1168-0.0891-0.1002-00.33270.0609-0.07330.3221-0.04320.2322-20.971-3.6016110.4781
31.08220.41740.19290.74790.27790.66260.1250.0686-0.0394-0.1128-0.03680.1126-0.33410.116100.28080.007-0.02090.2236-0.04980.2114-16.12833.1752119.2134
40.71860.2611-0.16371.11550.24890.6099-0.0356-0.1354-0.00020.2024-0.02150.03760.0359-0.0424-00.22410.0055-0.02520.2612-0.02660.2031-10.1015-13.230883.5468
50.0992-0.20740.35181.3247-0.42720.41310.01520.01580.0204-0.0231-0.0262-0.0476-0.0001-0.0133-00.1518-0.00860.00070.16670.00830.1873-19.5629-14.643246.777
60.221-0.17320.68150.9674-0.46721.5052-0.0906-0.0740.08680.103-0.0018-0.0364-0.2583-0.1516-00.21420.0166-0.01990.2364-0.06580.231-12.28677.17680.0096
70.3892-0.3681-0.05920.86090.15870.7383-0.020.0723-0.01310.04530.04550.09570.0474-0.0014-00.1712-0.00380.02440.14670.01570.1863-28.8662-3.960753.7131
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 52 through 115 )A52 - 115
2X-RAY DIFFRACTION2chain 'A' and (resid 116 through 163 )A116 - 163
3X-RAY DIFFRACTION3chain 'A' and (resid 164 through 263 )A164 - 263
4X-RAY DIFFRACTION4chain 'L' and (resid 2 through 109 )L2 - 109
5X-RAY DIFFRACTION5chain 'L' and (resid 110 through 213 )L110 - 213
6X-RAY DIFFRACTION6chain 'H' and (resid 1 through 136 )H1 - 136
7X-RAY DIFFRACTION7chain 'H' and (resid 137 through 231 )H137 - 231

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