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- PDB-1f58: IGG1 FAB FRAGMENT (58.2) COMPLEX WITH 24-RESIDUE PEPTIDE (RESIDUE... -

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Basic information

Entry
Database: PDB / ID: 1f58
TitleIGG1 FAB FRAGMENT (58.2) COMPLEX WITH 24-RESIDUE PEPTIDE (RESIDUES 308-333 OF HIV-1 GP120 (MN ISOLATE) WITH ALA TO AIB SUBSTITUTION AT POSITION 323
Components
  • Envelope glycoprotein gp120
  • PROTEIN (IGG1 ANTIBODY 58.2 (HEAVY CHAIN))
  • PROTEIN (IGG1 ANTIBODY 58.2 (LIGHT CHAIN))
KeywordsViral protein/Immune system / IMMUNOGLOBULIN / FAB / HIV-1 / GP120 / V3 / Viral protein-Immune system COMPLEX
Function / homology
Function and homology information


Dectin-2 family / immunoglobulin complex / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / adaptive immune response / viral protein processing / immune response / fusion of virus membrane with host plasma membrane ...Dectin-2 family / immunoglobulin complex / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / adaptive immune response / viral protein processing / immune response / 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 / metal ion binding / identical protein binding / membrane
Similarity search - Function
: / Envelope glycoprotein Gp160 / : / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin V-Type / Immunoglobulin V-set domain ...: / Envelope glycoprotein Gp160 / : / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig kappa chain V-III region PC 7183 / Envelope glycoprotein gp160 / Igh protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Human immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsStanfield, R.L. / Cabezas, E. / Satterthwait, A.C. / Stura, E.A. / Profy, A.T. / Wilson, I.A.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Dual conformations for the HIV-1 gp120 V3 loop in complexes with different neutralizing fabs.
Authors: Stanfield, R. / Cabezas, E. / Satterthwait, A. / Stura, E. / Profy, A. / Wilson, I.
History
DepositionOct 21, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Feb 2, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 22, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_nat / pdbx_entity_src_syn / pdbx_struct_mod_residue / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_mutation ..._entity.pdbx_description / _entity.pdbx_mutation / _entity_name_com.name / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_mod_residue.details / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.4Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: PROTEIN (IGG1 ANTIBODY 58.2 (LIGHT CHAIN))
H: PROTEIN (IGG1 ANTIBODY 58.2 (HEAVY CHAIN))
P: Envelope glycoprotein gp120


Theoretical massNumber of molelcules
Total (without water)51,1633
Polymers51,1633
Non-polymers00
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-28 kcal/mol
Surface area20100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.890, 71.910, 88.250
Angle α, β, γ (deg.)90.00, 98.31, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody PROTEIN (IGG1 ANTIBODY 58.2 (LIGHT CHAIN)) / FAB 58.2


Mass: 23573.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB-C / References: UniProt: P01666*PLUS
#2: Antibody PROTEIN (IGG1 ANTIBODY 58.2 (HEAVY CHAIN)) / FAB 58.2


Mass: 24864.744 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB-C / References: UniProt: Q99LC4*PLUS
#3: Protein/peptide Envelope glycoprotein gp120 / Env polyprotein


Mass: 2725.223 Da / Num. of mol.: 1 / Fragment: RESIDUES 308-332 FROM HIV-1 GP120 / Source method: obtained synthetically / Details: THE MOLECULE WAS CHEMICALLY SYNTHESIZED
Source: (synth.) Human immunodeficiency virus type 1 group M subtype B
References: UniProt: P05877
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FAB FRAGMENT IS NUMBERED BY THE CONVENTION OF E. KABAT (E.A. KABAT, T.T. WU, M. REID-MILLER, H. ...THE FAB FRAGMENT IS NUMBERED BY THE CONVENTION OF E. KABAT (E.A. KABAT, T.T. WU, M. REID-MILLER, H.M. PERRY, K.S. GOTTESMAN, SEQUENCES OF PROTEINS OF IMMUNOLOGICAL INTEREST, 4TH ED., (1987), NATIONAL INSTITUTE OF HEALTH, BETHESDA, MD.) THE PEPTIDE IS NUMBERED ACCORDING TO THE BH10 ISOLATE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 46 %
Crystal growpH: 6.3 / Details: pH 6.3
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 22.5 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
116 %PEG100001reservoir
20.2 Mimidazole malate1reservoir
315 mg/mlFab1drop

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 15, 1994 / Details: SUPER LONG MIRRORS (SIEMENS)
RadiationMonochromator: GRAPHITE(RIGAKU), SUPPER LONG MIRRORS (SIEMENS)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→43.6 Å / Num. obs: 30460 / % possible obs: 99.6 % / Redundancy: 10.4 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 29.5
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.547 / Mean I/σ(I) obs: 3.4 / % possible all: 98.5
Reflection
*PLUS
Num. measured all: 183103
Reflection shell
*PLUS
% possible obs: 98.5 % / Num. unique obs: 2014 / Num. measured obs: 9505

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MERLOTphasing
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FAB 58.2 PORTION OF FAB 58.2/SER-LOOP PEPTIDE COMPLEX

Resolution: 2→44 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.256 3024 9.9 %RANDOM
Rwork0.196 ---
obs0.196 30460 99.6 %-
Displacement parametersBiso mean: 23.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3497 0 0 120 3617
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.57
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.741.5
X-RAY DIFFRACTIONx_mcangle_it2.812
X-RAY DIFFRACTIONx_scbond_it3.172
X-RAY DIFFRACTIONx_scangle_it4.442.5
LS refinement shellResolution: 2→2.05 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.382 203 10.1 %
Rwork0.318 1811 -
obs--98.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.57
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.382 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.318 / Rfactor obs: 0.318

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