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- PDB-4m1d: Crystal structure of anti-HIV-1 Fab 447-52D in complex with V3 cy... -

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Basic information

Entry
Database: PDB / ID: 4m1d
TitleCrystal structure of anti-HIV-1 Fab 447-52D in complex with V3 cyclic peptide MN
Components
  • Cyclic V3 Arch Peptide
  • Fab mAb 447-52D Heavy Chain
  • Fab mAb 447-52D Light Chain
KeywordsIMMUNE SYSTEM / HIV / V3 LOOP / ANTIBODY-ANTIGEN INTERACTIONS / ENVELOPE
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 / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / immune response / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / immune response / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / extracellular space / 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 / 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/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Lambda-chain (AA -20 to 215) / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKillikelly, A. / Kong, X.P.
CitationJournal: Biochemistry / Year: 2013
Title: Thermodynamic Signatures of the Antigen Binding Site of mAb 447-52D Targeting the Third Variable Region of HIV-1 gp120.
Authors: Killikelly, A. / Zhang, H.T. / Spurrier, B. / Williams, C. / Gorny, M.K. / Zolla-Pazner, S. / Kong, X.P.
History
DepositionAug 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab mAb 447-52D Light Chain
H: Fab mAb 447-52D Heavy Chain
P: Cyclic V3 Arch Peptide
M: Fab mAb 447-52D Light Chain
I: Fab mAb 447-52D Heavy Chain
Q: Cyclic V3 Arch Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,86123
Polymers98,2966
Non-polymers1,56617
Water19,0961060
1
L: Fab mAb 447-52D Light Chain
H: Fab mAb 447-52D Heavy Chain
P: Cyclic V3 Arch Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,25315
Polymers49,1483
Non-polymers1,10512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7240 Å2
ΔGint-34 kcal/mol
Surface area20940 Å2
MethodPISA
2
M: Fab mAb 447-52D Light Chain
I: Fab mAb 447-52D Heavy Chain
Q: Cyclic V3 Arch Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6088
Polymers49,1483
Non-polymers4605
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-34 kcal/mol
Surface area21300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.836, 59.781, 137.066
Angle α, β, γ (deg.)90.00, 127.35, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Fab mAb 447-52D Light Chain


Mass: 22787.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: A2NUT2*PLUS
#2: Antibody Fab mAb 447-52D Heavy Chain


Mass: 24763.775 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein/peptide Cyclic V3 Arch Peptide


Mass: 1596.898 Da / Num. of mol.: 2 / Source method: obtained synthetically / References: UniProt: P05877*PLUS
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1060 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.71 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4
Details: pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 28, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. obs: 134437 / % possible obs: 93.9 %
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.63-1.66149.5
1.66-1.69168.9
1.69-1.72181.7
1.72-1.76191.9
1.76-1.79197
1.79-1.84198.5
1.84-1.88199
1.88-1.93199.2
1.93-1.99199.4
1.99-2.05199.3
2.05-2.13199
2.13-2.21199.3
2.21-2.31199
2.31-2.43199.2
2.43-2.59199.5
2.59-2.79199.7
2.79-3.07199.7
3.07-3.51199.8
3.51-4.42199.9
4.42-50198.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→45.341 Å / SU ML: 0.2 / σ(F): 1.35 / Phase error: 22.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2162 5302 4.98 %Automatically generated
Rwork0.186 ---
obs0.1875 106410 98.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→45.341 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6878 0 101 1060 8039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077139
X-RAY DIFFRACTIONf_angle_d1.1619690
X-RAY DIFFRACTIONf_dihedral_angle_d12.5072511
X-RAY DIFFRACTIONf_chiral_restr0.0791095
X-RAY DIFFRACTIONf_plane_restr0.0051221
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82050.29291810.26453301X-RAY DIFFRACTION98
1.8205-1.84190.28511610.26343291X-RAY DIFFRACTION98
1.8419-1.86430.26811700.25863383X-RAY DIFFRACTION98
1.8643-1.88790.26951490.25063313X-RAY DIFFRACTION98
1.8879-1.91280.26431730.26863307X-RAY DIFFRACTION98
1.9128-1.9390.26321620.23793336X-RAY DIFFRACTION98
1.939-1.96670.30031750.23043374X-RAY DIFFRACTION99
1.9667-1.9960.28981710.22053367X-RAY DIFFRACTION99
1.996-2.02720.26431870.21163295X-RAY DIFFRACTION99
2.0272-2.06050.24731840.2073394X-RAY DIFFRACTION99
2.0605-2.0960.24641760.20633306X-RAY DIFFRACTION99
2.096-2.13410.24291660.19983394X-RAY DIFFRACTION99
2.1341-2.17520.24841730.19823328X-RAY DIFFRACTION99
2.1752-2.21960.23511630.2033414X-RAY DIFFRACTION99
2.2196-2.26780.24081790.20173300X-RAY DIFFRACTION98
2.2678-2.32060.24971650.20013370X-RAY DIFFRACTION99
2.3206-2.37860.23521900.1973345X-RAY DIFFRACTION99
2.3786-2.44290.2521940.20233327X-RAY DIFFRACTION99
2.4429-2.51480.22551820.19673412X-RAY DIFFRACTION99
2.5148-2.59590.21281800.19193396X-RAY DIFFRACTION99
2.5959-2.68870.25211680.19873377X-RAY DIFFRACTION99
2.6887-2.79630.24441910.20213375X-RAY DIFFRACTION100
2.7963-2.92360.21471680.18953400X-RAY DIFFRACTION99
2.9236-3.07770.2241690.19013422X-RAY DIFFRACTION100
3.0777-3.27050.2431930.17933403X-RAY DIFFRACTION100
3.2705-3.52290.18971890.16773427X-RAY DIFFRACTION100
3.5229-3.87730.15951660.14993411X-RAY DIFFRACTION100
3.8773-4.43790.14921810.14193455X-RAY DIFFRACTION100
4.4379-5.58960.15922050.14473443X-RAY DIFFRACTION100
5.5896-45.35570.2381910.19763442X-RAY DIFFRACTION97

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