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- PDB-5drz: Crystal structure of anti-HIV-1 antibody F240 Fab in complex with... -

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Basic information

Entry
Database: PDB / ID: 5drz
TitleCrystal structure of anti-HIV-1 antibody F240 Fab in complex with gp41 peptide
Components
  • Envelope glycoprotein gp160
  • HIV Antibody F240 Heavy Chain
  • HIV Antibody F240 Light Chain
KeywordsIMMUNE SYSTEM / IgG / VIRAL PROTEIN / HIV gp41 ENVELOPE PROTEIN
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 ...: / 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
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_ARV2/SF2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsGohain, N. / Tolbert, W.D. / Pazgier, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1033109 United States
CitationJournal: Sci Rep / Year: 2016
Title: Molecular basis for epitope recognition by non-neutralizing anti-gp41 antibody F240.
Authors: Gohain, N. / Tolbert, W.D. / Orlandi, C. / Richard, J. / Ding, S. / Chen, X. / Bonsor, D.A. / Sundberg, E.J. / Lu, W. / Ray, K. / Finzi, A. / Lewis, G.K. / Pazgier, M.
History
DepositionSep 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: HIV Antibody F240 Light Chain
H: HIV Antibody F240 Heavy Chain
A: HIV Antibody F240 Light Chain
B: HIV Antibody F240 Heavy Chain
Q: Envelope glycoprotein gp160
P: Envelope glycoprotein gp160
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,8637
Polymers106,8396
Non-polymers241
Water2,756153
1
L: HIV Antibody F240 Light Chain
H: HIV Antibody F240 Heavy Chain
P: Envelope glycoprotein gp160
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4444
Polymers53,4203
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: HIV Antibody F240 Light Chain
B: HIV Antibody F240 Heavy Chain
Q: Envelope glycoprotein gp160


Theoretical massNumber of molelcules
Total (without water)53,4203
Polymers53,4203
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.317, 60.488, 169.228
Angle α, β, γ (deg.)90.00, 94.13, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.770664, -0.025536, 0.63673), (-0.026459, -0.999617, -0.008066), (0.636692, -0.010631, -0.771045)-24.89372, 0.64049, 68.72703

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Components

#1: Antibody HIV Antibody F240 Light Chain


Mass: 24363.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK-293 / Production host: Homo sapiens (human)
#2: Antibody HIV Antibody F240 Heavy Chain


Mass: 24970.748 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK-293 / Production host: Homo sapiens (human)
#3: Protein/peptide Envelope glycoprotein gp160 / Env polyprotein


Mass: 4085.668 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HIV-1 M:B_ARV2/SF2 (virus) / References: UniProt: P03378
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 25% PEG 3350, 15% Isopropanol, 0.2M Ammonium citrate pH4.5
PH range: 4.0-5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9753 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 4, 2013 / Details: RH coated flat mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9753 Å / Relative weight: 1
ReflectionResolution: 2.54→168.79 Å / Num. all: 33289 / Num. obs: 33289 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.158 / Net I/σ(I): 9.4
Reflection shellResolution: 2.54→2.58 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.957 / Mean I/σ(I) obs: 1.4 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TNN

3tnn


Resolution: 2.54→168.79 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.894 / SU B: 29.977 / SU ML: 0.298 / Cross valid method: THROUGHOUT / ESU R: 0.996 / ESU R Free: 0.325 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2585 1649 5.1 %RANDOM
Rwork0.20369 ---
obs0.20649 30876 98.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.223 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å2-0.15 Å2
2---0.71 Å20 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 2.54→168.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7031 0 1 153 7185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197229
X-RAY DIFFRACTIONr_bond_other_d0.0020.026633
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.9399837
X-RAY DIFFRACTIONr_angle_other_deg0.968315296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1575920
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.48523.821301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.719151137
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7051538
X-RAY DIFFRACTIONr_chiral_restr0.0780.21103
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028240
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021690
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_it0.92.5573680
X-RAY DIFFRACTIONr_mcbond_other0.92.5563679
X-RAY DIFFRACTIONr_mcangle_it1.6163.834594
X-RAY DIFFRACTIONr_mcangle_other1.6163.8314595
X-RAY DIFFRACTIONr_scbond_it0.82.6073549
X-RAY DIFFRACTIONr_scbond_other0.82.6073550
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4043.8685242
X-RAY DIFFRACTIONr_long_range_B_refined3.94423.8729139
X-RAY DIFFRACTIONr_long_range_B_other3.93723.86229103
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.541→2.607 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 113 -
Rwork0.353 2164 -
obs--92.15 %
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)
12.9822-0.0269-1.48150.64780.12432.0634-0.0716-0.1906-0.07050.02030.0246-0.00220.08690.0840.0470.0336-0.0028-0.04790.04640.03350.09495.2143-11.053279.4978
21.82270.4077-0.89610.7005-0.14691.7342-0.08440.2775-0.0362-0.11130.0730.02430.1149-0.13850.01140.0382-0.0023-0.03250.1150.02740.1063-7.0001-8.269266.4
31.18440.1110.05041.1455-0.0913.8996-0.01150.00850.0181-0.1552-0.0487-0.0808-0.2670.16770.06020.0453-0.0204-0.00930.07270.03910.166330.336810.728310.7308
40.8103-0.0658-0.430.9421-0.26912.0050.01430.04590.0293-0.08990.07980.086-0.1669-0.3006-0.0940.053-0.0114-0.05210.15110.03450.161112.47288.283813.3006
59.6131-3.7882-2.45035.6734-0.34141.0353-0.242-1.20420.96530.1160.4449-0.4950.08040.3142-0.20290.25110.0054-0.01780.3618-0.02860.141117.52613.747143.8233
63.40940.42675.70445.9764-2.169411.00850.15370.3145-0.0784-0.118-0.131-0.57890.40110.5333-0.02270.1696-0.04070.03750.33040.05290.390616.4638-3.72746.0618
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L2 - 211
2X-RAY DIFFRACTION2H1 - 215
3X-RAY DIFFRACTION3A2 - 213
4X-RAY DIFFRACTION4B1 - 215
5X-RAY DIFFRACTION5Q595 - 609
6X-RAY DIFFRACTION6P595 - 609

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