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- PDB-6ofi: CRYSTAL STRUCTURE OF the RV144 C1-C2 SPECIFIC ANTIBODY CH55 FAB I... -

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Basic information

Entry
Database: PDB / ID: 6ofi
TitleCRYSTAL STRUCTURE OF the RV144 C1-C2 SPECIFIC ANTIBODY CH55 FAB IN COMPLEX WITH HIV-1 CLADE A/E GP120
Components
  • CH55 Fab heavy chain
  • CH55 Fab light chain
  • clade A/E 93TH057 HIV-1 gp120 core
KeywordsIMMUNE SYSTEM / ANTI-HIV-1 ENV ANTIBODY CH55 / CD4I ANTIBODY / ADCC / HIV-1 ENV / RV144 VACCINE TRIAL / CLADE A/E 93TH057 / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX
Function / homologyGp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / viral envelope / clade A/E 93TH057 HIV-1 gp120 core
Function and homology information
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.85 Å
AuthorsTolbert, W.D. / Yan, F. / Van, V. / Pazgier, M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI116274 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI120756 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI129769 United States
CitationJournal: Mbio / Year: 2020
Title: Recognition Patterns of the C1/C2 Epitopes Involved in Fc-Mediated Response in HIV-1 Natural Infection and the RV114 Vaccine Trial.
Authors: Tolbert, W.D. / Van, V. / Sherburn, R. / Tuyishime, M. / Yan, F. / Nguyen, D.N. / Stanfield-Oakley, S. / Easterhoff, D. / Bonsignori, M. / Haynes, B.F. / Moody, M.A. / Ray, K. / Ferrari, G. ...Authors: Tolbert, W.D. / Van, V. / Sherburn, R. / Tuyishime, M. / Yan, F. / Nguyen, D.N. / Stanfield-Oakley, S. / Easterhoff, D. / Bonsignori, M. / Haynes, B.F. / Moody, M.A. / Ray, K. / Ferrari, G. / Lewis, G.K. / Pazgier, M.
History
DepositionMar 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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 / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
G: clade A/E 93TH057 HIV-1 gp120 core
H: CH55 Fab heavy chain
L: CH55 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,01813
Polymers86,8063
Non-polymers2,21210
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint-0 kcal/mol
Surface area34290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.644, 90.644, 408.994
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein clade A/E 93TH057 HIV-1 gp120 core


Mass: 39356.613 Da / Num. of mol.: 1 / Mutation: H375S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: HIV-1 Env / Cell (production host): HEK 293 GnT1- / Production host: Homo sapiens (human) / References: UniProt: A0A0M3KKW9
#2: Antibody CH55 Fab heavy chain


Mass: 24004.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK 293 / Production host: Homo sapiens (human)
#3: Antibody CH55 Fab light chain


Mass: 23444.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK 293 / Production host: Homo sapiens (human)
#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.: 10
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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.97 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 15% PEG 6000, 0.1 M sodium citrate pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 28, 2018
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.85→50 Å / Num. obs: 8672 / % possible obs: 81.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.249 / Net I/σ(I): 4.7
Reflection shellResolution: 3.85→3.92 Å / Redundancy: 3.3 % / Num. unique obs: 448 / CC1/2: 0.449 / Rpim(I) all: 0.567 / % possible all: 89.6

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OED, 3TGT

6oed

3tgt


Resolution: 3.85→41.43 Å / SU ML: 0.74 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.22
RfactorNum. reflection% reflection
Rfree0.326 414 4.82 %
Rwork0.271 --
obs0.274 8595 81.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.85→41.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5717 0 140 0 5857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056004
X-RAY DIFFRACTIONf_angle_d1.0618180
X-RAY DIFFRACTIONf_dihedral_angle_d6.93561
X-RAY DIFFRACTIONf_chiral_restr0.057943
X-RAY DIFFRACTIONf_plane_restr0.0071041
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8145-4.3660.3751320.32142819X-RAY DIFFRACTION87
4.366-5.49860.33991500.25712704X-RAY DIFFRACTION83
5.4986-41.43650.29521320.25712658X-RAY DIFFRACTION75
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)
12.7353-0.08231.84910.33-0.31633.5954-0.4611-0.27820.26380.17970.07840.1606-0.5308-0.563501.0064-0.05130.00730.7538-0.07370.8624-15.3898-22.8343-6.4682
21.39191.08670.36973.16760.42830.11890.05090.3635-0.1347-0.10490.0188-0.1690.25820.557700.20990.05270.03130.6213-0.00040.319530.5128-8.79620.612
32.15380.6444-0.92622.04530.63991.0166-0.1616-0.17160.1660.38240.1288-0.0696-0.07630.4739-00.25080.1271-0.05790.3487-0.00710.265623.06291.015634.6266
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN 'G' AND RESID 44 THROUGH 492)
2X-RAY DIFFRACTION2(CHAIN 'H' AND RESID 1 THROUGH 213)
3X-RAY DIFFRACTION3(CHAIN 'L' AND RESID 1 THROUGH 212)

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