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- PDB-4r4f: Crystal structure of non-neutralizing, A32-like antibody 2.2c in ... -

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Basic information

Entry
Database: PDB / ID: 4r4f
TitleCrystal structure of non-neutralizing, A32-like antibody 2.2c in complex with HIV-1 YU2 gp120
Components
  • (Antibody 2.2c ...) x 2
  • HIV-1 Env gp120
  • M48U1 peptide
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM/INHIBITOR / HIV-1 attachment protein / Membrane / VIRAL PROTEIN-IMMUNE SYSTEM-INHIBITOR complex
Function / homology
Function and homology information


Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 / virion attachment to host cell ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / 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
CD4-MIMETIC MINIPROTEIN M48U1 / (R,R)-2,3-BUTANEDIOL / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.514 Å
AuthorsAcharya, P. / Kwong, P.D.
CitationJournal: J.Virol. / Year: 2014
Title: Structural Definition of an Antibody-Dependent Cellular Cytotoxicity Response Implicated in Reduced Risk for HIV-1 Infection.
Authors: Acharya, P. / Tolbert, W.D. / Gohain, N. / Wu, X. / Yu, L. / Liu, T. / Huang, W. / Huang, C.C. / Kwon, Y.D. / Louder, R.K. / Luongo, T.S. / McLellan, J.S. / Pancera, M. / Yang, Y. / Zhang, B. ...Authors: Acharya, P. / Tolbert, W.D. / Gohain, N. / Wu, X. / Yu, L. / Liu, T. / Huang, W. / Huang, C.C. / Kwon, Y.D. / Louder, R.K. / Luongo, T.S. / McLellan, J.S. / Pancera, M. / Yang, Y. / Zhang, B. / Flinko, R. / Foulke, J.S. / Sajadi, M.M. / Kamin-Lewis, R. / Robinson, J.E. / Martin, L. / Kwong, P.D. / Guan, Y. / DeVico, A.L. / Lewis, G.K. / Pazgier, M.
History
DepositionAug 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Structure summary
Revision 1.2Oct 22, 2014Group: Database references
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
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 / _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.pdbx_value_order / _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 1.5Sep 20, 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 1.6Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.7Jan 10, 2024Group: Derived calculations / Category: struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 Env gp120
L: Antibody 2.2c LIGHT CHAIN
H: Antibody 2.2c heavy CHAIN
R: M48U1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,40017
Polymers91,1684
Non-polymers2,23213
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7420 Å2
ΔGint-41 kcal/mol
Surface area35800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.321, 171.230, 227.974
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

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Antibody , 2 types, 2 molecules LH

#2: Antibody Antibody 2.2c LIGHT CHAIN


Mass: 22839.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody Antibody 2.2c heavy CHAIN


Mass: 23576.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Protein / Protein/peptide / Sugars , 3 types, 10 molecules AR

#1: Protein HIV-1 Env gp120


Mass: 41695.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli (E. coli) / References: UniProt: P35961*PLUS
#4: Protein/peptide M48U1 peptide


Type: Peptide-like / Class: Inhibitor / Mass: 3056.804 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: CD4-MIMETIC MINIPROTEIN M48U1
#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.: 8
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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Non-polymers , 2 types, 5 molecules

#6: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

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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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.24 Å3/Da / Density % sol: 70.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10% MPD, 1.5 M lithium sulfate and 100 mM Imidazole pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 11, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. all: 19484 / Num. obs: 16141 / % possible obs: 85.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 2 / % possible all: 59.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JZZ

4jzz


Resolution: 3.514→35.754 Å / SU ML: 0.69 / Isotropic thermal model: Isotropic / σ(F): 1.33 / Phase error: 43.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2948 1627 10.16 %
Rwork0.2505 --
obs0.2549 16015 82.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.514→35.754 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6146 0 140 0 6286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076444
X-RAY DIFFRACTIONf_angle_d1.1068751
X-RAY DIFFRACTIONf_dihedral_angle_d22.663899
X-RAY DIFFRACTIONf_chiral_restr0.0551008
X-RAY DIFFRACTIONf_plane_restr0.0071110
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.514-3.61710.7783560.7053518X-RAY DIFFRACTION36
3.6171-3.73380.4774950.4822837X-RAY DIFFRACTION59
3.7338-3.86710.40771130.4161976X-RAY DIFFRACTION67
3.8671-4.02170.38631150.34331071X-RAY DIFFRACTION75
4.0217-4.20450.39391390.32711187X-RAY DIFFRACTION82
4.2045-4.42570.3221490.26831255X-RAY DIFFRACTION88
4.4257-4.70250.29141500.24241296X-RAY DIFFRACTION90
4.7025-5.06460.28111490.2231370X-RAY DIFFRACTION93
5.0646-5.57260.27041670.23521426X-RAY DIFFRACTION98
5.5726-6.3750.32781610.25331452X-RAY DIFFRACTION100
6.375-8.01690.29981640.26521488X-RAY DIFFRACTION100
8.0169-35.7560.23611690.20161512X-RAY DIFFRACTION98
Refinement TLS params.

S33: -0 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9321-0.30691.02043.0931-0.81382.2001-0.33210.27340.3372-0.23950.2344-0.601-0.93391.30421.9919-0.60240.09912.8549-0.14132.6796-18.1501-20.32543.2935
20.0915-0.1670.0780.2084-0.01130.03451.0133-1.17480.15671.88350.9245-1.4665-0.51380.25922.46450.45120.18524.1644-0.1613.0584-14.1835-31.154661.934
34.34050.73010.6990.1456-0.25983.5212-0.39420.170.1481-0.07030.34150.0523-0.4438-0.38232.70740.11510.05911.5270.02192.2616-69.0704-14.397623.2633
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain R
3X-RAY DIFFRACTION3chain L or chain H

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