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- PDB-6oej: CRYSTAL STRUCTURE OF THE NON-NEUTRALIZING AND ADCC-POTENT ANTIBOD... -

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Basic information

Entry
Database: PDB / ID: 6oej
TitleCRYSTAL STRUCTURE OF THE NON-NEUTRALIZING AND ADCC-POTENT ANTIBODY C11 IN COMPLEX WITH HIV-1 CLADE A/E GP120
Components
  • C11 Fab heavy chain
  • C11 Fab light chain
  • clade A/E 93TH057 HIV-1 gp120 core
KeywordsIMMUNE SYSTEM / HIV-1 GP120 / CLADE A/E 93TH057 / VIRAL PROTEIN / 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: 3.45 Å
AuthorsTolbert, 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
DepositionMar 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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 / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _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 / 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: C11 Fab heavy chain
L: C11 Fab light chain
A: clade A/E 93TH057 HIV-1 gp120 core
B: C11 Fab heavy chain
C: C11 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,74430
Polymers184,4126
Non-polymers6,33224
Water0
1
G: clade A/E 93TH057 HIV-1 gp120 core
H: C11 Fab heavy chain
L: C11 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,37215
Polymers92,2063
Non-polymers3,16612
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8570 Å2
ΔGint17 kcal/mol
Surface area38020 Å2
MethodPISA
2
A: clade A/E 93TH057 HIV-1 gp120 core
B: C11 Fab heavy chain
C: C11 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,37215
Polymers92,2063
Non-polymers3,16612
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8640 Å2
ΔGint25 kcal/mol
Surface area38410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.371, 110.961, 217.563
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 42852.781 Da / Num. of mol.: 2 / Mutation: H375S, S31C, N80C
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: Antibody C11 Fab heavy chain


Mass: 25642.584 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)
#3: Antibody C11 Fab light chain


Mass: 23710.502 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: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 22
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
Sequence detailsAUTHOR STATES THAT THE REFERENCE SEQUENCE FROM THE DATABASE REPRESENTS A TRUNCATED VERSION OF THE ...AUTHOR STATES THAT THE REFERENCE SEQUENCE FROM THE DATABASE REPRESENTS A TRUNCATED VERSION OF THE FULL LENGTH HIV ENV SEQUENCE. NUMBERING OF THE GP120 IS BASED ON THE HXBC2 ENV. CHAINS G AND A BOTH HAVE A HISTIDINE TO SERINE MUTATION AT POSITION 375 IN THE STRUCTURE. RESIDUES 31-43 AND 493-511 ARE THE FULL LENGTH N AND C-TERMINI OF THE SEQUENCE REFERENCED IN THE DATABASE. CYS 31 is also an engineered mutation (originally SER in sequence)

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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: 2.92 Å3/Da / Density % sol: 57.95 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 17% PEG 6000 0.1 M sodium citrate pH 5.0

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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: Jul 29, 2017
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.45→50 Å / Num. obs: 26654 / % possible obs: 91.3 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.117 / Net I/σ(I): 6.6
Reflection shellResolution: 3.45→3.51 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.685 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1270 / CC1/2: 0.55 / Rpim(I) all: 0.496 / % 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: 4FZ8, 3TGT

4fz8

3tgt


Resolution: 3.45→49.424 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2841 1312 4.93 %
Rwork0.2309 --
obs0.2337 26621 91.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.45→49.424 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11734 0 406 0 12140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00412455
X-RAY DIFFRACTIONf_angle_d0.85316994
X-RAY DIFFRACTIONf_dihedral_angle_d5.937326
X-RAY DIFFRACTIONf_chiral_restr0.0651983
X-RAY DIFFRACTIONf_plane_restr0.0062149
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4502-3.58830.32281370.27152750X-RAY DIFFRACTION91
3.5883-3.75150.32071420.26152931X-RAY DIFFRACTION96
3.7515-3.94920.35781620.24722847X-RAY DIFFRACTION94
3.9492-4.19650.30591480.22272895X-RAY DIFFRACTION94
4.1965-4.52040.30681510.20682739X-RAY DIFFRACTION90
4.5204-4.97490.25971580.19762798X-RAY DIFFRACTION91
4.9749-5.69380.2621440.21462824X-RAY DIFFRACTION91
5.6938-7.17010.27891250.27062715X-RAY DIFFRACTION86
7.1701-49.42870.25281450.22842810X-RAY DIFFRACTION86
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)
13.20070.00871.44063.2247-0.2944.90840.106-0.72380.31150.99410.0725-0.2259-0.58160.4267-0.17440.91-0.09790.10871.04530.06371.0306-20.4209-4.360651.2629
23.55910.2087-1.49292.833-1.63133.64830.06690.4574-0.4042-0.1861-0.1390.0139-0.0329-0.12340.07410.29710.079-0.02730.4257-0.08750.6721-20.71458.0881-6.9715
32.91111.7219-2.28433.1517-1.92752.561-0.16770.2864-0.6075-0.2611-0.1496-0.12160.3012-0.03020.33710.33410.0862-0.11470.5508-0.10650.753-8.3096-3.3953-12.8418
42.32190.64092.40673.54450.02492.8139-0.1280.5310.1626-1.0340.20810.1663-0.31420.0319-0.10130.9820.14150.22661.1656-0.01271.214118.96151.1435-48.2802
53.4288-0.4255-2.17972.35531.01683.80030.2157-0.5256-0.14440.1388-0.1185-0.5176-0.11690.2293-0.09210.3477-0.0708-0.15430.39620.05090.746219.40466.908610.9986
62.9285-2.1393-1.57422.94751.44642.1638-0.0933-0.1557-0.57240.2718-0.06860.10990.18410.0030.16390.3741-0.1323-0.02680.49640.13160.81966.9561-5.045215.509
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'G' and resid 31 through 497)
2X-RAY DIFFRACTION2(chain 'H' and resid 1 through 215)
3X-RAY DIFFRACTION3(chain 'L' and resid 1 through 211)
4X-RAY DIFFRACTION4(chain 'A' and resid 31 through 497)
5X-RAY DIFFRACTION5(chain 'B' and resid 1 through 215)
6X-RAY DIFFRACTION6(chain 'C' and resid 1 through 212)

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