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- PDB-2qsc: Crystal structure analysis of anti-HIV-1 V3-Fab F425-B4e8 in comp... -

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Basic information

Entry
Database: PDB / ID: 2qsc
TitleCrystal structure analysis of anti-HIV-1 V3-Fab F425-B4e8 in complex with a V3-peptide
Components
  • (Fab F425-B4e8, ...) x 2
  • Envelope glycoprotein gp120
KeywordsIMMUNE SYSTEM / Fab-peptide complex / HIV-1 / gp120 / V3 loop / immunoglobulin fold / AIDS / Apoptosis / Envelope protein / Fusion protein / Glycoprotein / Host-virus interaction / Membrane / Transmembrane / Viral immunoevasion / Virion
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsBell, C.H. / Schiefner, A. / Stanfield, R.L. / Wilson, I.A.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structure of antibody F425-B4e8 in complex with a V3 peptide reveals a new binding mode for HIV-1 neutralization.
Authors: Bell, C.H. / Pantophlet, R. / Schiefner, A. / Cavacini, L.A. / Stanfield, R.L. / Burton, D.R. / Wilson, I.A.
History
DepositionJul 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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 / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_ref_seq / 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 / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _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 / _struct_conn_type.id / _struct_ref_seq.db_align_end
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: Fab F425-B4e8, Light chain
H: Fab F425-B4e8, Heavy chain
P: Envelope glycoprotein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,82212
Polymers48,8323
Non-polymers9909
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.912, 39.858, 97.960
Angle α, β, γ (deg.)90.00, 108.50, 90.00
Int Tables number3
Space group name H-MP121

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Components

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Antibody , 2 types, 2 molecules LH

#1: Antibody Fab F425-B4e8, Light chain


Mass: 23325.727 Da / Num. of mol.: 1 / Fragment: Light chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HMMA myeloma cells / Production host: Homo sapiens (human)
#2: Antibody Fab F425-B4e8, Heavy chain


Mass: 23728.277 Da / Num. of mol.: 1 / Fragment: Heavy chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HMMA myeloma cells / Production host: Homo sapiens (human)

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

#3: Protein/peptide Envelope glycoprotein gp120 / / Env polyprotein


Mass: 1778.090 Da / Num. of mol.: 1 / Fragment: Residues 301-326 / Source method: obtained synthetically
Details: THIS SEQUENCE OCCURS IN HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (ISOLATE MN)
References: UniProt: P05877
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 23 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 3.14 Å3/Da / Density % sol: 60.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6
Details: PEG 8000, pH 6.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 1, 2007 / Details: Rh coated flat mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 15169 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 60.8 Å2 / Rsym value: 0.102 / Net I/σ(I): 12.6
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.476 / % possible all: 94.6

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.883 / SU B: 29.893 / SU ML: 0.286 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.38 / ESU R Free: 0.368 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.264 755 5 %RANDOM
Rwork0.219 ---
obs0.222 15169 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.742 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å21.78 Å2
2--3.43 Å20 Å2
3----1.55 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3353 0 47 15 3415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0223484
X-RAY DIFFRACTIONr_angle_refined_deg0.9461.9624740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.255435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.38524.196143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6415537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.551515
X-RAY DIFFRACTIONr_chiral_restr0.060.2543
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022608
X-RAY DIFFRACTIONr_nbd_refined0.1720.21308
X-RAY DIFFRACTIONr_nbtor_refined0.2980.22292
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.2121
X-RAY DIFFRACTIONr_metal_ion_refined0.0670.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0280.23
X-RAY DIFFRACTIONr_mcbond_it0.1471.52231
X-RAY DIFFRACTIONr_mcangle_it0.26723525
X-RAY DIFFRACTIONr_scbond_it0.43531415
X-RAY DIFFRACTIONr_scangle_it0.824.51215
LS refinement shellResolution: 2.8→2.877 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 48 -
Rwork0.33 1000 -
all-1048 -
obs--92.99 %
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)
12.95430.8808-1.88042.7702-2.55995.42180.0428-0.0818-0.1133-0.09750.06010.12940.0167-0.2901-0.103-0.25160.01230.0101-0.1514-0.0494-0.1708-10.90093.048525.9848
25.17082.62690.88165.42271.37443.28650.1312-0.69680.2790.3497-0.05370.0707-0.48980.3837-0.0776-0.1531-0.01470.02220.1498-0.0224-0.19554.41998.396459.8482
32.74270.82930.55443.3720.78745.5177-0.04610.0467-0.09890.04440.0147-0.3365-0.40650.20850.0314-0.12070.0550.0516-0.23440.0286-0.16475.625914.877319.5903
46.3563-0.2790.18537.66391.0914.8375-0.0058-0.3195-0.1007-0.0528-0.0239-0.2747-0.29040.51740.0297-0.2201-0.03260.0118-0.0265-0.0453-0.166915.07789.363946.9202
510.08597.25064.12768.0634-3.175314.92330.1826-0.51121.4458-1.1604-0.06630.6206-0.44580.0937-0.11630.09110.08630.0828-0.02460.0501-0.2376-6.185515.37114.8193
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 108
2X-RAY DIFFRACTION2L109 - 214
3X-RAY DIFFRACTION3H1 - 123
4X-RAY DIFFRACTION4H124 - 222
5X-RAY DIFFRACTION5P304 - 318

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