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- PDB-6q1e: Inferred precursor (UCA) of the human antibody lineage 652 -

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Basic information

Entry
Database: PDB / ID: 6q1e
TitleInferred precursor (UCA) of the human antibody lineage 652
Components
  • Fab heavy chain
  • Fab lambda chain
KeywordsIMMUNE SYSTEM / antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 3, 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 1.2Oct 23, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab lambda chain
H: Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)48,8962
Polymers48,8962
Non-polymers00
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-21 kcal/mol
Surface area19950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.440, 69.670, 74.440
Angle α, β, γ (deg.)90.000, 100.080, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Fab lambda chain


Mass: 22960.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293T / Production host: Homo sapiens (human)
#2: 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) / Cell line (production host): 293T / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
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: 2.37 Å3/Da / Density % sol: 48.16 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 5% (v/v) PEG 400, 1.4M sodium citrate pH 5.0

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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: Dec 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→44.738 Å / Num. obs: 15923 / % possible obs: 99.67 % / Redundancy: 3.7 % / CC1/2: 0.993 / Rmerge(I) obs: 0.1316 / Net I/σ(I): 10.85
Reflection shellResolution: 2.5→2.589 Å / Rmerge(I) obs: 1.031 / Num. unique obs: 1576 / CC1/2: 0.579

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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: 2.5→44.738 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.49
RfactorNum. reflection% reflection
Rfree0.2574 807 5.07 %
Rwork0.2227 --
obs0.2245 15914 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.22 Å2 / Biso mean: 44.6372 Å2 / Biso min: 16.06 Å2
Refinement stepCycle: final / Resolution: 2.5→44.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3293 0 0 91 3384
Biso mean---37.2 -
Num. residues----441
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5001-2.65680.37861270.3222250599
2.6568-2.86190.34371360.30712508100
2.8619-3.14980.29851380.25532476100
3.1498-3.60540.28741350.23692516100
3.6054-4.54170.22241310.18542534100
4.5417-44.730.19971400.18022568100
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)
10.54250.10470.33720.07380.2811.2292-0.17350.1042-0.06040.95020.0777-0.08990.33650.2939-0.0250.62750.0057-0.04190.23570.00770.3477-16.2534-30.6553-3.1927
20.51330.11510.32320.6762-0.15530.2730.05960.0673-0.31410.03020.0687-0.0287-0.1692-0.06780.01180.42960.01660.06630.35210.02450.2873-22.8531-24.5704-13.0589
30.8379-0.4021-0.16030.41950.01440.07170.11310.1332-0.05370.4183-0.0304-0.0934-0.2794-0.22520.09670.45030.00760.05520.25990.04690.2958-14.1734-28.0981-11.5924
40.5781-0.6528-0.10510.69620.08370.70790.20030.05590.5715-0.0030.1268-0.082-0.05570.04720.13590.1227-0.0067-0.00760.3142-0.00570.368910.7545-26.1954-29.7464
50.2091-0.10060.25050.61870.36980.72170.1553-0.03110.1197-0.10190.1796-0.37280.02340.30070.23540.17640.00980.01390.38640.00790.384518.616-29.8743-35.0206
61.0302-0.65820.08760.83040.22660.21310.0490.1464-0.24290.8635-0.01910.1647-0.1514-0.0481-0.04620.5607-0.0584-0.04260.44490.04290.2816-9.7943-3.3939-19.2028
71.33220.3209-0.37680.9987-0.57410.3653-0.05070.1461-0.050.61710.02360.1146-0.2777-0.0767-0.04010.61670.04120.08070.2710.0210.2767-18.8778-6.6359-10.6957
80.3627-0.1203-0.36440.5242-0.58491.361-0.1668-0.0027-0.2012-0.0719-0.09670.00550.04430.2355-0.77260.098-0.0098-0.07940.31080.00990.30092.9097-17.2973-33.2919
90.51730.2095-0.18860.1737-0.22890.5615-0.21690.1372-0.0433-0.220.1053-0.1168-0.1688-0.0502-0.01860.1959-0.0238-0.00210.2541-0.02660.3414-0.3079-16.6703-42.3798
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 3 through 28 )H3 - 28
2X-RAY DIFFRACTION2chain 'H' and (resid 29 through 60 )H29 - 60
3X-RAY DIFFRACTION3chain 'H' and (resid 61 through 121 )H61 - 121
4X-RAY DIFFRACTION4chain 'H' and (resid 122 through 183 )H122 - 183
5X-RAY DIFFRACTION5chain 'H' and (resid 184 through 212 )H184 - 212
6X-RAY DIFFRACTION6chain 'L' and (resid 1 through 17 )L1 - 17
7X-RAY DIFFRACTION7chain 'L' and (resid 18 through 126 )L18 - 126
8X-RAY DIFFRACTION8chain 'L' and (resid 127 through 194 )L127 - 194
9X-RAY DIFFRACTION9chain 'L' and (resid 195 through 231 )L195 - 231

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