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- PDB-5tfs: Structure of chimeric 02-K Fab, a VRC01-like germline antibody -

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Basic information

Entry
Database: PDB / ID: 5tfs
TitleStructure of chimeric 02-K Fab, a VRC01-like germline antibody
Components
  • 02-K Fab Heavy chain
  • 02-K Fab Light chain
KeywordsIMMUNE SYSTEM / Fab / HIV-1 / VRC01 / CDRH3 / CD4-BS / Vh1-2
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.319 Å
AuthorsPancera, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)2R01 AI081625 United States
CitationJournal: Cell Rep / Year: 2016
Title: Differences in Allelic Frequency and CDRH3 Region Limit the Engagement of HIV Env Immunogens by Putative VRC01 Neutralizing Antibody Precursors.
Authors: Yacoob, C. / Pancera, M. / Vigdorovich, V. / Oliver, B.G. / Glenn, J.A. / Feng, J. / Sather, D.N. / McGuire, A.T. / Stamatatos, L.
History
DepositionSep 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Dec 11, 2019Group: Author supporting evidence / Polymer sequence / Category: entity_poly / pdbx_audit_support
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: 02-K Fab Heavy chain
L: 02-K Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8466
Polymers46,4622
Non-polymers3844
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-92 kcal/mol
Surface area19060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.525, 81.295, 121.719
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Antibody 02-K Fab Heavy chain


Mass: 23340.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody 02-K Fab Light chain


Mass: 23121.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

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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: 293 K / Method: vapor diffusion, hanging drop
Details: 30 % PEG 8000, 15 % isopropanol, 0.1 M Hepes pH 7.5, 0.2 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.319→44.27 Å / Num. obs: 21164 / % possible obs: 99.7 % / Redundancy: 7 % / Net I/σ(I): 16.5

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.319→44.27 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.88
RfactorNum. reflection% reflection
Rfree0.2279 1063 5.04 %
Rwork0.2013 --
obs0.2027 21088 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.319→44.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3240 0 20 137 3397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033345
X-RAY DIFFRACTIONf_angle_d0.6234557
X-RAY DIFFRACTIONf_dihedral_angle_d12.6261980
X-RAY DIFFRACTIONf_chiral_restr0.044502
X-RAY DIFFRACTIONf_plane_restr0.003577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3191-2.42460.31031200.2622443X-RAY DIFFRACTION99
2.4246-2.55240.26521180.23632478X-RAY DIFFRACTION100
2.5524-2.71230.27991350.24042468X-RAY DIFFRACTION100
2.7123-2.92170.26081390.24182475X-RAY DIFFRACTION100
2.9217-3.21570.22271230.22922489X-RAY DIFFRACTION100
3.2157-3.68080.24331250.19952518X-RAY DIFFRACTION100
3.6808-4.63660.20331530.16762503X-RAY DIFFRACTION100
4.6366-44.27820.19711500.17992651X-RAY DIFFRACTION100
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)
11.8434-1.8092-0.39122.68061.95222.60930.1920.06540.01950.1584-0.0934-1.04790.09340.2186-0.14040.2877-0.0291-0.0390.3532-0.01130.374-33.6235104.0012189.3053
22.7874-0.07430.93863.27190.90734.6873-0.02630.0956-0.07480.09170.04120.0621-0.10530.0806-0.02090.37-0.00380.03720.27460.02830.2523-45.4509106.8401190.5291
32.9325-0.39941.2184.47831.29044.9762-0.0341-0.1609-0.44690.29920.08260.76640.6106-0.2707-0.09370.4887-0.02210.06480.29050.03880.3378-46.4234101.2796199.142
41.7314-1.62020.78632.44940.58352.3534-0.00870.0622-0.05830.15410.1-0.02150.00170.1234-0.10560.362-0.05390.02420.31430.01320.3208-41.4559105.4526191.417
52.6805-1.184-0.83043.8023-0.25133.4165-0.00890.34210.055-0.58730.2772-0.0850.35150.4765-0.4010.3391-0.1247-0.01660.4789-0.08820.5114-29.622890.2241165.1739
60.9647-0.70090.26043.15170.43325.6312-0.030.12790.2938-0.38530.1375-0.2746-0.4950.6057-0.24910.4704-0.12870.08760.4492-0.03990.5117-28.606795.1647163.9986
71.4621-0.56090.78883.9704-0.65176.57810.24350.27650.2722-0.4890.1141-0.5218-0.78260.9474-0.32110.513-0.11120.12440.4842-0.07460.4762-27.770995.7017160.6551
83.93490.8645-0.20564.9880.9455.60250.2369-0.1793-0.42450.4073-0.03570.5338-0.0007-0.6286-0.18380.42530.0384-0.04740.41830.01270.5831-61.598104.5833176.4661
93.2632-1.94541.21326.27280.94174.15620.09520.12840.1559-0.1962-0.26270.2892-0.2725-0.11750.19390.37650.0119-0.02410.2875-0.0060.2521-56.4983113.0654176.9775
103.2433-0.53330.24274.6078-0.6118.66-0.10360.1539-0.0145-0.0162-0.14590.1735-0.3918-0.30280.19420.38-0.006-0.03650.2826-0.060.4267-54.8826107.3797175.5723
112.2048-1.72180.18333.43240.49742.6199-0.0116-0.1585-0.0384-0.21770.1239-0.15480.07160.1565-0.10990.4431-0.03920.03150.3631-0.01610.3009-40.674486.4499157.8803
122.8738-0.306-0.05752.58590.80762.9977-0.0387-0.1017-0.12460.0570.10170.06380.07620.2343-0.09530.43210.01510.03020.31970.0230.2723-39.764784.1079155.464
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 2 through 25 )
2X-RAY DIFFRACTION2chain 'H' and (resid 26 through 51 )
3X-RAY DIFFRACTION3chain 'H' and (resid 52 through 66 )
4X-RAY DIFFRACTION4chain 'H' and (resid 67 through 106 )
5X-RAY DIFFRACTION5chain 'H' and (resid 107 through 134 )
6X-RAY DIFFRACTION6chain 'H' and (resid 135 through 157 )
7X-RAY DIFFRACTION7chain 'H' and (resid 158 through 213 )
8X-RAY DIFFRACTION8chain 'L' and (resid 2 through 33 )
9X-RAY DIFFRACTION9chain 'L' and (resid 34 through 75 )
10X-RAY DIFFRACTION10chain 'L' and (resid 76 through 102 )
11X-RAY DIFFRACTION11chain 'L' and (resid 103 through 165 )
12X-RAY DIFFRACTION12chain 'L' and (resid 166 through 213 )

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