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- PDB-6ol7: Crystal structure of glVRC01 scFv in complex with anti-idiotype i... -

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Basic information

Entry
Database: PDB / ID: 6ol7
TitleCrystal structure of glVRC01 scFv in complex with anti-idiotype iv8 scFv
Components
  • glVRC01 Heavy Chain
  • glVRC01 Light Chain
  • iv8 Heavy Chain
  • iv8 Light Chain
KeywordsIMMUNE SYSTEM / glVRC01 / Iv8 / Anti-Idiotype / scFv / antibody / HIV
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.419 Å
AuthorsWeidle, C. / Pancera, M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HIVRAD/1P01AI138212 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI081625 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI138212 United States
CitationJournal: J.Exp.Med. / Year: 2019
Title: Anti-idiotypic antibodies elicit anti-HIV-1-specific B cell responses.
Authors: Dosenovic, P. / Pettersson, A.K. / Wall, A. / Thientosapol, E.S. / Feng, J. / Weidle, C. / Bhullar, K. / Kara, E.E. / Hartweger, H. / Pai, J.A. / Gray, M.D. / Parks, K.R. / Taylor, J.J. / ...Authors: Dosenovic, P. / Pettersson, A.K. / Wall, A. / Thientosapol, E.S. / Feng, J. / Weidle, C. / Bhullar, K. / Kara, E.E. / Hartweger, H. / Pai, J.A. / Gray, M.D. / Parks, K.R. / Taylor, J.J. / Pancera, M. / Stamatatos, L. / Nussenzweig, M.C. / McGuire, A.T.
History
DepositionApr 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: iv8 Heavy Chain
B: glVRC01 Light Chain
C: glVRC01 Heavy Chain
D: iv8 Light Chain
E: iv8 Heavy Chain
F: glVRC01 Light Chain
H: glVRC01 Heavy Chain
I: glVRC01 Heavy Chain
J: iv8 Light Chain
K: iv8 Heavy Chain
L: glVRC01 Light Chain
M: glVRC01 Heavy Chain
N: glVRC01 Light Chain
O: iv8 Light Chain
P: iv8 Heavy Chain
Q: iv8 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,42656
Polymers220,55616
Non-polymers2,87040
Water20,6631147
1
A: iv8 Heavy Chain
H: glVRC01 Heavy Chain
L: glVRC01 Light Chain
Q: iv8 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,72412
Polymers55,1394
Non-polymers5858
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: glVRC01 Light Chain
C: glVRC01 Heavy Chain
D: iv8 Light Chain
E: iv8 Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,57311
Polymers55,1394
Non-polymers4347
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
F: glVRC01 Light Chain
I: glVRC01 Heavy Chain
J: iv8 Light Chain
K: iv8 Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,20218
Polymers55,1394
Non-polymers1,06314
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
M: glVRC01 Heavy Chain
N: glVRC01 Light Chain
O: iv8 Light Chain
P: iv8 Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,92715
Polymers55,1394
Non-polymers78811
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.583, 107.937, 116.961
Angle α, β, γ (deg.)85.49, 80.28, 84.17
Int Tables number1
Space group name H-MP1

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Components

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Antibody , 4 types, 16 molecules AEKPBFLNCHIMDJOQ

#1: Antibody
iv8 Heavy Chain


Mass: 14527.015 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody
glVRC01 Light Chain


Mass: 11673.807 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Antibody
glVRC01 Heavy Chain


Mass: 15607.272 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#4: Antibody
iv8 Light Chain


Mass: 13330.836 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 1187 molecules

#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1147 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.98 Å3/Da / Density % sol: 58.68 % / Description: plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.13M NaCl, 0.13M Tris pH 8.0, 10.4% PEG 20,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.419→50 Å / Num. obs: 87182 / % possible obs: 92.39 % / Redundancy: 1.7 % / Net I/σ(I): 10.25
Reflection shellResolution: 2.419→2.506 Å / Num. unique obs: 5909

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MFT

6mft


Resolution: 2.419→49.784 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 25.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2238 4370 5.01 %
Rwork0.1743 --
obs0.1767 87139 92.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.419→49.784 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14344 0 184 1147 15675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214868
X-RAY DIFFRACTIONf_angle_d0.49620082
X-RAY DIFFRACTIONf_dihedral_angle_d18.0585312
X-RAY DIFFRACTIONf_chiral_restr0.0422121
X-RAY DIFFRACTIONf_plane_restr0.0022542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4188-2.44630.2605760.21111600X-RAY DIFFRACTION52
2.4463-2.47510.2677980.20631883X-RAY DIFFRACTION64
2.4751-2.50530.28271150.22882113X-RAY DIFFRACTION71
2.5053-2.5370.32351400.23712320X-RAY DIFFRACTION78
2.537-2.57040.29461220.22182750X-RAY DIFFRACTION91
2.5704-2.60560.30441550.21862774X-RAY DIFFRACTION93
2.6056-2.64280.29851560.20932733X-RAY DIFFRACTION93
2.6428-2.68220.31011450.21532803X-RAY DIFFRACTION93
2.6822-2.72420.26921910.21082818X-RAY DIFFRACTION95
2.7242-2.76880.27631320.20542814X-RAY DIFFRACTION95
2.7688-2.81650.29351510.20412783X-RAY DIFFRACTION94
2.8165-2.86780.27111530.20072914X-RAY DIFFRACTION96
2.8678-2.92290.24731220.19512830X-RAY DIFFRACTION96
2.9229-2.98260.25531400.19392893X-RAY DIFFRACTION96
2.9826-3.04740.25581570.19272913X-RAY DIFFRACTION97
3.0474-3.11830.24111450.192876X-RAY DIFFRACTION97
3.1183-3.19630.27071360.19762959X-RAY DIFFRACTION97
3.1963-3.28270.27291460.18932895X-RAY DIFFRACTION97
3.2827-3.37920.22711380.18892968X-RAY DIFFRACTION98
3.3792-3.48830.22351530.17182909X-RAY DIFFRACTION98
3.4883-3.61290.21911590.17012873X-RAY DIFFRACTION97
3.6129-3.75750.21161700.16152896X-RAY DIFFRACTION98
3.7575-3.92850.20471370.15822960X-RAY DIFFRACTION98
3.9285-4.13550.21181620.14492921X-RAY DIFFRACTION98
4.1355-4.39450.17041580.12772905X-RAY DIFFRACTION98
4.3945-4.73350.1541650.11572940X-RAY DIFFRACTION98
4.7335-5.20940.14561740.12292911X-RAY DIFFRACTION98
5.2094-5.96210.17391640.15522905X-RAY DIFFRACTION99
5.9621-7.50750.2321610.19662971X-RAY DIFFRACTION99
7.5075-49.79440.19871490.18682939X-RAY DIFFRACTION98

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