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- PDB-4rfn: Crystal structure of ADCC-potent Rhesus macaque ANTIBODY JR4 in c... -

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Entry
Database: PDB / ID: 4rfn
TitleCrystal structure of ADCC-potent Rhesus macaque ANTIBODY JR4 in complex with HIV-1 CLADE A/E GP120 and M48
Components
  • FAB HEAVY CHAIN OF ADCC ANTI-HIV-1 ANTIBODY JR4
  • FAB LIGHT CHAIN OF ADCC ANTI-HIV-1 ANTIBODY JR4
  • HIV-1 CLADE A/E 93TH057 (H375S) GP120
  • T-CELL SURFACE GLYCOPROTEIN CD4 mimetic M48
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HIV-1 GP120 / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / plasma membrane
Similarity search - Function
HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Beta Complex / Immunoglobulins ...HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Beta Complex / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Macaca mulatta (Rhesus monkey)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å
AuthorsGohain, N. / Tolbert, W.D. / Pazgier, M.
CitationJournal: J.Virol. / Year: 2015
Title: Cocrystal Structures of Antibody N60-i3 and Antibody JR4 in Complex with gp120 Define More Cluster A Epitopes Involved in Effective Antibody-Dependent Effector Function against HIV-1.
Authors: Gohain, N. / Tolbert, W.D. / Acharya, P. / Yu, L. / Liu, T. / Zhao, P. / Orlandi, C. / Visciano, M.L. / Kamin-Lewis, R. / Sajadi, M.M. / Martin, L. / Robinson, J.E. / Kwong, P.D. / DeVico, A. ...Authors: Gohain, N. / Tolbert, W.D. / Acharya, P. / Yu, L. / Liu, T. / Zhao, P. / Orlandi, C. / Visciano, M.L. / Kamin-Lewis, R. / Sajadi, M.M. / Martin, L. / Robinson, J.E. / Kwong, P.D. / DeVico, A.L. / Ray, K. / Lewis, G.K. / Pazgier, M.
History
DepositionSep 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
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 / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jun 2, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.host_org_common_name ..._chem_comp.pdbx_synonyms / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_vector_type
Revision 1.4Sep 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: HIV-1 CLADE A/E 93TH057 (H375S) GP120
H: FAB HEAVY CHAIN OF ADCC ANTI-HIV-1 ANTIBODY JR4
L: FAB LIGHT CHAIN OF ADCC ANTI-HIV-1 ANTIBODY JR4
M: T-CELL SURFACE GLYCOPROTEIN CD4 mimetic M48
A: HIV-1 CLADE A/E 93TH057 (H375S) GP120
B: FAB HEAVY CHAIN OF ADCC ANTI-HIV-1 ANTIBODY JR4
C: FAB LIGHT CHAIN OF ADCC ANTI-HIV-1 ANTIBODY JR4
D: T-CELL SURFACE GLYCOPROTEIN CD4 mimetic M48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,32626
Polymers179,3448
Non-polymers3,98218
Water0
1
G: HIV-1 CLADE A/E 93TH057 (H375S) GP120
H: FAB HEAVY CHAIN OF ADCC ANTI-HIV-1 ANTIBODY JR4
L: FAB LIGHT CHAIN OF ADCC ANTI-HIV-1 ANTIBODY JR4
M: T-CELL SURFACE GLYCOPROTEIN CD4 mimetic M48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,66313
Polymers89,6724
Non-polymers1,9919
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9900 Å2
ΔGint-2 kcal/mol
Surface area34240 Å2
MethodPISA
2
A: HIV-1 CLADE A/E 93TH057 (H375S) GP120
B: FAB HEAVY CHAIN OF ADCC ANTI-HIV-1 ANTIBODY JR4
C: FAB LIGHT CHAIN OF ADCC ANTI-HIV-1 ANTIBODY JR4
D: T-CELL SURFACE GLYCOPROTEIN CD4 mimetic M48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,66313
Polymers89,6724
Non-polymers1,9919
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10010 Å2
ΔGint-2 kcal/mol
Surface area34150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.255, 77.827, 127.587
Angle α, β, γ (deg.)90.00, 114.26, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein HIV-1 CLADE A/E 93TH057 (H375S) GP120


Mass: 39160.367 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 line (production host): HEK 293 GnT1- / Production host: Homo sapiens (human) / References: UniProt: Q0ED31*PLUS
#2: Antibody FAB HEAVY CHAIN OF ADCC ANTI-HIV-1 ANTIBODY JR4


Mass: 24847.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey)
Gene: Fab heavy chain of ADCC-potent anti-HIV-1 antibody JR4
Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#3: Antibody FAB LIGHT CHAIN OF ADCC ANTI-HIV-1 ANTIBODY JR4


Mass: 22719.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey)
Gene: Fab light chain of ADCC-potent anti-HIV-1 antibody JR4
Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#4: Protein/peptide T-CELL SURFACE GLYCOPROTEIN CD4 mimetic M48


Mass: 2944.634 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: M48 is an engineered CD4 mimetic / Source: (synth.) synthetic construct (others)
#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.: 18
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
Nonpolymer detailsTHE DENSITY ALONG WITH THE BIOCHEMICAL DATA SUPPORT THE INCLUSION OF THE NAG'S IN CHAINS A AND G ...THE DENSITY ALONG WITH THE BIOCHEMICAL DATA SUPPORT THE INCLUSION OF THE NAG'S IN CHAINS A AND G EVEN THOUGH THE NAGS HAVE POOR ELECTRON DENSITY

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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: 2.77 Å3/Da / Density % sol: 55.62 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.1271 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 16, 2012 / Details: RH coated flat mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 3.17→50 Å / Num. obs: 33553 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.252 / Net I/σ(I): 6.9
Reflection shellResolution: 3.17→3.23 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.871 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4RFE for JR4, PDB entry 4H8W for gp120, PDB entry 2I5Y for M48

4rfe

4h8w

2i5y


Resolution: 3.21→45 Å / Cor.coef. Fo:Fc: 0.884 / Cor.coef. Fo:Fc free: 0.81 / SU B: 124.273 / SU ML: 0.848 / Cross valid method: THROUGHOUT / ESU R Free: 0.686 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33226 1643 5 %RANDOM
Rwork0.27335 ---
obs0.27623 30928 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 94.681 Å2
Baniso -1Baniso -2Baniso -3
1--7.72 Å2-0 Å21.18 Å2
2--0.49 Å2-0 Å2
3---4.39 Å2
Refinement stepCycle: LAST / Resolution: 3.21→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12086 0 252 0 12338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01912656
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211742
X-RAY DIFFRACTIONr_angle_refined_deg1.1481.96717104
X-RAY DIFFRACTIONr_angle_other_deg0.794327036
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.39251528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.23425.082488
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.792152014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4721536
X-RAY DIFFRACTIONr_chiral_restr0.0620.21996
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02113792
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022712
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_it0.5412.3476305
X-RAY DIFFRACTIONr_mcbond_other0.542.3466303
X-RAY DIFFRACTIONr_mcangle_it0.9813.5247746
X-RAY DIFFRACTIONr_mcangle_other0.877.1297861
X-RAY DIFFRACTIONr_scbond_it2.1032.666345
X-RAY DIFFRACTIONr_scbond_other0.4514.7926379
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.7677.1769437
X-RAY DIFFRACTIONr_long_range_B_refined1.66845.20350998
X-RAY DIFFRACTIONr_long_range_B_other1.66845.20350999
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.21→3.291 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 123 -
Rwork0.359 2269 -
obs--99.79 %
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)
11.7918-0.0234-1.12832.61310.3274.9884-0.03990.02680.00870.43110.05430.66720.6622-0.6802-0.01441.918-0.06050.17510.28660.02490.175823.0046-14.748623.927
21.69030.4931.38812.1753-0.10274.25580.0171-0.1055-0.05050.2942-0.0771-0.6641-0.51580.6290.061.948-0.0512-0.00980.27190.02920.2188-22.116421.841224.4082
314.95551.6464-11.75492.2904-1.56839.28590.33970.28710.3846-0.48480.00950.6343-0.1205-0.297-0.34921.2173-0.00350.04331.0504-0.05861.17958.72641.161732.2408
44.8057-0.80137.30141.8986-0.927811.14690.05710.1099-0.0808-0.45670.2117-0.8029-0.04190.2461-0.26881.0487-0.00710.06271.0706-0.00071.1033-8.13535.757532.6422
51.03330.51890.45942.14141.53066.16170.00310.16240.0903-0.17360.10810.19020.01190.2406-0.11121.50560.0667-0.02440.05580.02260.040135.6654-12.5407-28.7499
61.27690.3780.07532.2206-2.26277.22420.08430.2565-0.1573-0.15120.1807-0.0572-0.0318-0.0776-0.2651.26850.10920.18160.1394-0.04340.0684-36.534419.8846-27.9763
70.7871-0.08480.00121.18220.26656.15090.04530.1904-0.03580.0389-0.0092-0.28330.40390.7048-0.03611.44670.1333-0.03860.2454-0.02620.078844.2041-26.6513-26.6783
80.6423-0.16270.09812.160.33984.7781-0.03010.2642-0.03960.10060.12820.45-0.3678-0.6581-0.0981.53460.18050.21940.31260.07280.1234-44.418834.0888-25.2176
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1G44 - 492
2X-RAY DIFFRACTION2A44 - 492
3X-RAY DIFFRACTION3M2 - 27
4X-RAY DIFFRACTION4D2 - 27
5X-RAY DIFFRACTION5H1 - 212
6X-RAY DIFFRACTION6B1 - 212
7X-RAY DIFFRACTION7L3 - 208
8X-RAY DIFFRACTION8C3 - 208

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