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- PDB-6mfp: Crystal Structure of the RV305 C1-C2 specific ADCC potent antibod... -

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Basic information

Entry
Database: PDB / ID: 6mfp
TitleCrystal Structure of the RV305 C1-C2 specific ADCC potent antibody DH677.3 Fab in complex with HIV-1 clade A/E gp120 and M48U1
Components
  • DH677.3 Fab heavy chain
  • DH677.3 Fab light chain
  • M48U1 CD4 MIMETIC PEPTIDE
  • clade A/E 93TH057 HIV-1 gp120 core
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / ANTI-HIV-1 ENV ANTIBODY DH677.3 / CD4I ANTIBODY / ADCC / HIV-1 ENV / IMMUNE SYSTEM / RV305 VACCINE TRIAL / HIV-1 GP120 / CLADE A/E 93TH057 / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


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: 3 Å
AuthorsTolbert, W.D. / Young, B. / Pazgier, M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI16274 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: J.Virol. / Year: 2020
Title: Boosting with AIDSVAX B/E Enhances Env Constant Region 1 and 2 Antibody-Dependent Cellular Cytotoxicity Breadth and Potency.
Authors: Easterhoff, D. / Pollara, J. / Luo, K. / Tolbert, W.D. / Young, B. / Mielke, D. / Jha, S. / O'Connell, R.J. / Vasan, S. / Kim, J. / Michael, N.L. / Excler, J.L. / Robb, M.L. / Rerks-Ngarm, S. ...Authors: Easterhoff, D. / Pollara, J. / Luo, K. / Tolbert, W.D. / Young, B. / Mielke, D. / Jha, S. / O'Connell, R.J. / Vasan, S. / Kim, J. / Michael, N.L. / Excler, J.L. / Robb, M.L. / Rerks-Ngarm, S. / Kaewkungwal, J. / Pitisuttithum, P. / Nitayaphan, S. / Sinangil, F. / Tartaglia, J. / Phogat, S. / Kepler, T.B. / Alam, S.M. / Wiehe, K. / Saunders, K.O. / Montefiori, D.C. / Tomaras, G.D. / Moody, M.A. / Pazgier, M. / Haynes, B.F. / Ferrari, G.
History
DepositionSep 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Derived calculations / Category: pdbx_struct_assembly_gen / Item: _pdbx_struct_assembly_gen.asym_id_list
Revision 1.2Nov 6, 2019Group: Data collection / Structure summary / Category: pdbx_entry_details / pdbx_molecule_features / Item: _pdbx_entry_details.compound_details
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Apr 1, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 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

Downloads & links

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Assembly

Deposited unit
G: clade A/E 93TH057 HIV-1 gp120 core
N: M48U1 CD4 MIMETIC PEPTIDE
H: DH677.3 Fab heavy chain
L: DH677.3 Fab light chain
A: clade A/E 93TH057 HIV-1 gp120 core
M: M48U1 CD4 MIMETIC PEPTIDE
C: DH677.3 Fab heavy chain
D: DH677.3 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,09734
Polymers180,3678
Non-polymers5,72926
Water00
1
G: clade A/E 93TH057 HIV-1 gp120 core
N: M48U1 CD4 MIMETIC PEPTIDE
H: DH677.3 Fab heavy chain
L: DH677.3 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,83816
Polymers90,1844
Non-polymers2,65412
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: clade A/E 93TH057 HIV-1 gp120 core
M: M48U1 CD4 MIMETIC PEPTIDE
C: DH677.3 Fab heavy chain
D: DH677.3 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,25818
Polymers90,1844
Non-polymers3,07514
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.487, 80.093, 88.688
Angle α, β, γ (deg.)84.82, 82.33, 82.24
Int Tables number1
Space group name H-MP1

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Components

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Antibody , 2 types, 4 molecules HCLD

#3: Antibody DH677.3 Fab heavy chain


Mass: 24504.537 Da / Num. of mol.: 2
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 DH677.3 Fab light chain


Mass: 23265.709 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK 293 / Production host: Homo sapiens (human)

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Protein / Protein/peptide / Non-polymers , 3 types, 6 molecules GANM

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


Mass: 39356.613 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: CD4-MIMETIC MINIPROTEIN M48U1
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl

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Sugars , 2 types, 24 molecules

#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: 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.: 23 / 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

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Details

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
Sequence detailsAuthors state that Val 42 and Pro 43 of HIV-1 gp120 core are missing from UNP A0A0M3KKW9 but are ...Authors state that Val 42 and Pro 43 of HIV-1 gp120 core are missing from UNP A0A0M3KKW9 but are part of the protein and not an expression tag

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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: 2.45 Å3/Da / Density % sol: 49.77 %
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: 3→50 Å / Num. obs: 30469 / % possible obs: 89.1 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 10.2
Reflection shellResolution: 3→3.05 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.442 / Num. unique obs: 1547 / % possible all: 90.7

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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: 3TGT, 6MFJ

3tgt

6mfj


Resolution: 3→39.6 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.905 / SU B: 79.988 / SU ML: 0.629 / Cross valid method: THROUGHOUT / ESU R Free: 0.576 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1492 4.9 %RANDOM
Rwork0.214 ---
obs0.217 28977 88.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 93.95 Å2
Baniso -1Baniso -2Baniso -3
1-1.84 Å21.48 Å2-3.11 Å2
2---0.25 Å2-1.24 Å2
3----2.01 Å2
Refinement stepCycle: LAST / Resolution: 3→39.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12342 0 362 0 12704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01313024
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711668
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.69217715
X-RAY DIFFRACTIONr_angle_other_deg1.1841.61427279
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.98151577
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.97723.833574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.934152080
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0441546
X-RAY DIFFRACTIONr_chiral_restr0.0530.21812
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214257
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022521
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_it2.5286.5666388
X-RAY DIFFRACTIONr_mcbond_other2.5286.5666387
X-RAY DIFFRACTIONr_mcangle_it4.1619.8227931
X-RAY DIFFRACTIONr_mcangle_other4.1619.8237932
X-RAY DIFFRACTIONr_scbond_it2.6886.976636
X-RAY DIFFRACTIONr_scbond_other2.6896.9696634
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.50910.369784
X-RAY DIFFRACTIONr_long_range_B_refined9.89150216
X-RAY DIFFRACTIONr_long_range_B_other9.89250212
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 104 -
Rwork0.327 2144 -
obs--87.81 %
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)
14.1975-0.18542.36812.4258-0.64623.84360.1617-0.25480.1638-0.2282-0.06440.18570.4135-0.6992-0.09730.1549-0.1358-0.07820.24090.05540.0567-4.7413-17.54032.5485
22.4809-0.79462.64321.2924-1.26583.4719-0.4122-0.91730.4910.50080.0958-0.2198-0.3968-0.68830.31640.30080.1028-0.19930.6108-0.23550.385425.1021-16.542849.7816
32.5873-0.95522.50831.1261-1.71274.78790.0087-0.33670.42440.0988-0.2586-0.43040.43590.14450.24990.2068-0.0361-0.17370.2490.04580.298838.1944-28.563545.0329
44.75140.2182-0.12331.54390.18944.10660.084-0.9275-0.23210.1586-0.0935-0.0332-0.20640.2520.00950.1335-0.1405-0.11460.30420.15640.123521.325820.168660.2263
55.4391-1.02522.38142.7492-0.97942.18660.38860.389-0.5621-0.7659-0.08640.75020.4609-0.134-0.30220.3883-0.0143-0.33090.1191-0.06480.3327-18.350611.584421.7658
63.9588-0.03891.75372.111-0.17012.2975-0.12980.24780.3256-0.42030.0830.74540.11-0.17440.04680.2343-0.0525-0.25420.07020.06010.3544-23.461329.259219.5054
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1G44 - 492
2X-RAY DIFFRACTION2H1 - 214
3X-RAY DIFFRACTION3L1 - 213
4X-RAY DIFFRACTION4A44 - 492
5X-RAY DIFFRACTION5C1 - 214
6X-RAY DIFFRACTION6D1 - 213

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