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- PDB-3uji: Crystal structure of anti-HIV-1 V3 Fab 2558 in complex with MN peptide -

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Basic information

Entry
Database: PDB / ID: 3uji
TitleCrystal structure of anti-HIV-1 V3 Fab 2558 in complex with MN peptide
Components
  • Envelope glycoprotein gp160
  • Fab region of the heavy chain of anti-HIV-1 V3 monoclonal antibody 2558
  • Light chain of anti-HIV-1 V3 monoclonal antibody 2558
KeywordsIMMUNE SYSTEM / Ig domains / antibody Fab / antigen binding / The third variable region of HIV-1 gp120
Function / homology
Function and homology information


Dectin-2 family / 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 ...Dectin-2 family / 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 / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane / identical protein binding
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
HIV-1 M:B_MN (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKong, X.P.
CitationJournal: Plos One / Year: 2011
Title: Human Anti-V3 HIV-1 Monoclonal Antibodies Encoded by the VH5-51/VL Lambda Genes Define a Conserved Antigenic Structure.
Authors: Gorny, M.K. / Sampson, J. / Li, H. / Jiang, X. / Totrov, M. / Wang, X.H. / Williams, C. / O'Neal, T. / Volsky, B. / Li, L. / Cardozo, T. / Nyambi, P. / Zolla-Pazner, S. / Kong, X.P.
History
DepositionNov 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
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 / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Light chain of anti-HIV-1 V3 monoclonal antibody 2558
H: Fab region of the heavy chain of anti-HIV-1 V3 monoclonal antibody 2558
P: Envelope glycoprotein gp160
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4245
Polymers48,8133
Non-polymers6112
Water12,899716
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-21 kcal/mol
Surface area19040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.351, 73.097, 88.662
Angle α, β, γ (deg.)90.00, 121.98, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Antibody , 2 types, 2 molecules LH

#1: Antibody Light chain of anti-HIV-1 V3 monoclonal antibody 2558


Mass: 22195.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Immune system / Source: (natural) Homo sapiens (human)
#2: Antibody Fab region of the heavy chain of anti-HIV-1 V3 monoclonal antibody 2558


Mass: 23906.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Immune system / Source: (natural) Homo sapiens (human)

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Protein/peptide / Sugars , 2 types, 2 molecules P

#3: Protein/peptide Envelope glycoprotein gp160 / Env polyprotein / Surface protein gp120 / SU / Glycoprotein 120 / gp120 / Transmembrane protein ...Env polyprotein / Surface protein gp120 / SU / Glycoprotein 120 / gp120 / Transmembrane protein gp41 / TM / Glycoprotein 41 / gp41


Mass: 2711.196 Da / Num. of mol.: 1 / Fragment: unp residues 306-328 / Source method: obtained synthetically / Source: (synth.) HIV-1 M:B_MN (virus) / References: UniProt: P05877
#4: 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: isolated from a genetically manipulated source
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

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Non-polymers , 2 types, 717 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 716 / Source method: isolated from a natural source / Formula: H2O

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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: 2.88 Å3/Da / Density % sol: 57.32 %
Crystal growTemperature: 296 K / Method: evaporation / pH: 7.5
Details: 85mM Hepes-Na, 15% Glycerol, 17% PEG 4k, 8.5% Isopropanol, pH 7.5, EVAPORATION, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97854 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 3, 2008
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97854 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 73190 / Num. obs: 72608 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.1 % / Rsym value: 0.054 / Net I/σ(I): 29.1
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.431 / % possible all: 98.4

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Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.362 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19378 3662 5 %RANDOM
Rwork0.16095 ---
obs0.1626 68884 99 %-
all-72546 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å2-0.28 Å2
2---0.32 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3358 0 39 716 4113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.023491
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.6331.9634762
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2515440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.99824.646127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89815533
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.034157
X-RAY DIFFRACTIONr_chiral_restr0.2150.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0212608
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.599→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 247 -
Rwork0.215 4943 -
obs--97.37 %

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