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- PDB-6mg7: Crystal structure of the RV144 C1-C2 specific antibody CH54 Fab i... -

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Basic information

Entry
Database: PDB / ID: 6mg7
TitleCrystal structure of the RV144 C1-C2 specific antibody CH54 Fab in complex with HIV-1 CLADE A/E GP120 and M48U1
Components
  • CH54 Fab heavy chain
  • CH54 Fab light chain
  • M48U1 CD4 mimetic peptide
  • clade A/E 93TH057 HIV-1 gp120 core
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / ANTI-HIV-1 ENV ANTIBODY CH54 / CD4I ANTIBODY / ADCC / HIV-1 ENV / IMMUNE SYSTEM / RV144 VACCINE TRIAL / CLADE A/E 93TH057 / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / viral envelope / symbiont entry into host cell / virion attachment to host cell / virion membrane
Similarity search - Function
Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CD4-MIMETIC MINIPROTEIN M48U1 / clade A/E 93TH057 HIV-1 gp120 core
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsVan, V. / Tolbert, W.D. / 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
DepositionSep 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Structure summary / Category: pdbx_entry_details / pdbx_molecule_features
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jul 15, 2020Group: Data collection / Database references / Structure summary
Category: audit_author / chem_comp ...audit_author / chem_comp / citation / citation_author
Item: _audit_author.name / _chem_comp.type ..._audit_author.name / _chem_comp.type / _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 1.4Jul 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 1.5Oct 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
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: clade A/E 93TH057 HIV-1 gp120 core
N: M48U1 CD4 mimetic peptide
H: CH54 Fab heavy chain
L: CH54 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,28614
Polymers92,0744
Non-polymers2,21210
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)174.827, 42.231, 119.754
Angle α, β, γ (deg.)90.00, 115.24, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 42847.676 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- cells / Production host: Homo sapiens (human) / References: UniProt: A0A0M3KKW9
#2: Protein/peptide M48U1 CD4 mimetic peptide


Type: Peptide-like / Class: Inhibitor / Mass: 3056.804 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: CD4-MIMETIC MINIPROTEIN M48U1
#3: Antibody CH54 Fab heavy chain


Mass: 23532.475 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: Antibody CH54 Fab light chain


Mass: 22637.182 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)
#5: 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: obtained synthetically / 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
Compound detailsTHE CD4-MIMETIC MINIPROTEINS INHIBIT HIV-1 ENTRY AND ARE DERIVED FROM SCYLLATOXIN (A SCORPION TOXIN) ...THE CD4-MIMETIC MINIPROTEINS INHIBIT HIV-1 ENTRY AND ARE DERIVED FROM SCYLLATOXIN (A SCORPION TOXIN) BY TRANSPLANTING THE GP120-INTERACTIVE REGION OF CD4 ONTO THE SCYLLATOXIN SCAFFOLD, FOLLOWED BY MANY ROUNDS OF ITERATIVE OPTIMIZATION

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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: 2.17 Å3/Da / Density % sol: 43.36 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 25% PEG 4000 0.1 M MES pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 25, 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: 2.9→50 Å / Num. obs: 16963 / % possible obs: 95.9 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.174 / Net I/σ(I): 11.1
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.833 / Mean I/σ(I) obs: 1 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RFO

4rfo


Resolution: 2.91→39.68 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.872 / SU B: 85.574 / SU ML: 0.71 / Cross valid method: THROUGHOUT / ESU R Free: 0.571 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.307 807 4.8 %RANDOM
Rwork0.25 ---
obs0.252 16155 94.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 89.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å2-0.23 Å2
2---1.94 Å20 Å2
3---0.9 Å2
Refinement stepCycle: LAST / Resolution: 2.91→39.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6027 0 140 0 6167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0136326
X-RAY DIFFRACTIONr_bond_other_d0.0020.0175700
X-RAY DIFFRACTIONr_angle_refined_deg1.6511.6868608
X-RAY DIFFRACTIONr_angle_other_deg1.3791.60513341
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6395772
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.7123.826264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.208151021
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2531521
X-RAY DIFFRACTIONr_chiral_restr0.0670.2887
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026885
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021200
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4475.4333132
X-RAY DIFFRACTIONr_mcbond_other2.4475.4333131
X-RAY DIFFRACTIONr_mcangle_it4.0128.1263885
X-RAY DIFFRACTIONr_mcangle_other4.0128.1263886
X-RAY DIFFRACTIONr_scbond_it2.8185.8953193
X-RAY DIFFRACTIONr_scbond_other2.8185.8953194
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7968.7344724
X-RAY DIFFRACTIONr_long_range_B_refined10.32124494
X-RAY DIFFRACTIONr_long_range_B_other10.32124492
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.91→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 39 -
Rwork0.352 1002 -
obs--78.63 %
Refinement TLS params.Method: refined / Origin x: -65.4168 Å / Origin y: 26.8542 Å / Origin z: -3.7151 Å
111213212223313233
T0.0198 Å2-0.0396 Å20.0136 Å2-0.5408 Å2-0.0338 Å2--0.2949 Å2
L0.7505 °2-0.2588 °20.8035 °2-0.5537 °2-0.5661 °2--2.0907 °2
S0.0128 Å °-0.0489 Å °-0.0316 Å °-0.0618 Å °0.0624 Å °0.0051 Å °0.156 Å °-0.1929 Å °-0.0752 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1G43 - 495
2X-RAY DIFFRACTION1H1 - 212
3X-RAY DIFFRACTION1L1 - 210

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