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- PDB-3c2a: Antibody Fab fragment 447-52D in complex with UG1033 peptide -

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Basic information

Entry
Database: PDB / ID: 3c2a
TitleAntibody Fab fragment 447-52D in complex with UG1033 peptide
Components
  • Envelope glycoprotein
  • Fab 447-52D heavy chain
  • Fab 447-52D light chain
KeywordsIMMUNE SYSTEM / antibody fab hiv-1 peptide / Envelope protein
Function / homology
Function and homology information


IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation ...IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / immunoglobulin mediated immune response / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / viral process / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / antigen binding / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / adaptive immune response / Potential therapeutics for SARS / blood microparticle / viral envelope / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / 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 ...Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / 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
Immunoglobulin lambda constant 3 / Glycoprotein 120
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDhillon, A.K. / Stanfield, R.L. / Wilson, I.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structure determination of an anti-HIV-1 Fab 447-52D-peptide complex from an epitaxially twinned data set
Authors: Dhillon, A.K. / Stanfield, R.L. / Gorny, M.K. / Williams, C. / Zolla-Pazner, S. / Wilson, I.A.
History
DepositionJan 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 9, 2018Group: Advisory / Data collection ...Advisory / Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_nat ...entity / entity_src_nat / pdbx_entity_src_syn / pdbx_unobs_or_zero_occ_atoms / struct
Item: _entity.pdbx_description / _entity_src_nat.pdbx_ncbi_taxonomy_id ..._entity.pdbx_description / _entity_src_nat.pdbx_ncbi_taxonomy_id / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _struct.pdbx_descriptor
Revision 1.3Aug 30, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab 447-52D light chain
H: Fab 447-52D heavy chain
P: Envelope glycoprotein
M: Fab 447-52D light chain
I: Fab 447-52D heavy chain
Q: Envelope glycoprotein


Theoretical massNumber of molelcules
Total (without water)97,9416
Polymers97,9416
Non-polymers00
Water3,369187
1
L: Fab 447-52D light chain
H: Fab 447-52D heavy chain
P: Envelope glycoprotein


Theoretical massNumber of molelcules
Total (without water)48,9713
Polymers48,9713
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-34.4 kcal/mol
Surface area21350 Å2
MethodPISA
2
M: Fab 447-52D light chain
I: Fab 447-52D heavy chain
Q: Envelope glycoprotein


Theoretical massNumber of molelcules
Total (without water)48,9713
Polymers48,9713
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-32.1 kcal/mol
Surface area21440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.251, 76.482, 114.130
Angle α, β, γ (deg.)90.00, 101.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Fab 447-52D light chain


Mass: 22787.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P0DOY3*PLUS
#2: Antibody Fab 447-52D heavy chain


Mass: 24763.775 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: Protein/peptide Envelope glycoprotein


Mass: 1419.651 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The peptide is naturally found in HIV-1 gp120. / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q9YWB6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 3.06 Å3/Da / Density % sol: 59.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 1.58M ammonium sulfate 0.1M Tris 1mM CuCl2, pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 25, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 60586 / Num. obs: 60586 / % possible obs: 85.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Rsym value: 0.084 / Net I/σ(I): 27.1
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 4 / Num. unique all: 3035 / Rsym value: 0.445 / % possible all: 86

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
Blu-Icedata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1q1j

1q1j


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.895 / SU B: 13.52 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.261 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29775 1395 2.3 %RANDOM
Rwork0.24 ---
obs0.2413 58014 85.66 %-
all-58014 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.165 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20.31 Å2
2--0.95 Å20 Å2
3----1.6 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6884 0 0 187 7071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0227056
X-RAY DIFFRACTIONr_angle_refined_deg1.6371.9539622
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2675914
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68624.048252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.885151088
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9991526
X-RAY DIFFRACTIONr_chiral_restr0.1090.21094
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025274
X-RAY DIFFRACTIONr_nbd_refined0.2170.22783
X-RAY DIFFRACTIONr_nbtor_refined0.3070.24705
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2391
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0910.210
X-RAY DIFFRACTIONr_mcbond_it0.7981.54654
X-RAY DIFFRACTIONr_mcangle_it1.30927364
X-RAY DIFFRACTIONr_scbond_it1.97632813
X-RAY DIFFRACTIONr_scangle_it2.8164.52258
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 99 -
Rwork0.299 4323 -
obs--86.88 %
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)
13.22961.4239-0.59042.6299-0.8441.4299-0.1082-0.1534-0.19390.0749-0.031-0.15680.09650.09650.1392-0.25030.0112-0.0326-0.1437-0.0279-0.11464.706359.548872.9161
23.0233-1.3088-2.63612.2441.71485.125-0.1126-0.0627-0.05680.20780.02530.01660.39590.2050.0872-0.2392-0.0081-0.0443-0.17820.0109-0.10397.180135.483251.6844
32.2769-0.1422-1.09263.1520.52953.71180.0346-0.11960.29260.16020.1170.0275-0.09520.0828-0.1516-0.2429-0.0401-0.0258-0.1931-0.0032-0.04518.448274.476959.3255
43.13842.6164-0.20813.49970.01282.773-0.03180.0126-0.2127-0.11340.0817-0.13810.0295-0.0365-0.0499-0.21090.03090.0044-0.18140.0034-0.1512-3.068538.182339.6178
50.3389-0.98030.44534.5455-1.67127.3273-0.10250.19020.0486-0.00420.0683-0.5719-0.75021.25660.0341-0.0256-0.1560.04910.193-0.13970.002321.978122.6723-8.8557
60.07610.1343-0.21343.92382.24619.54940.0675-0.06530.1171-0.60610.2922-0.5399-0.90781.1619-0.35970.0266-0.11820.13850.0951-0.09390.029615.978647.85811.5354
70.875-0.23310.23.48172.19067.76750.04980.0505-0.1484-0.09610.3603-0.25610.65480.7157-0.41010.02020.1334-0.08120.0403-0.11210.017519.0298.08465.2665
83.2479-2.14250.09663.741-1.46064.53610.04040.19160.3045-0.03470.1148-0.1707-0.28530.1819-0.1552-0.0734-0.0559-0.0083-0.1273-0.0057-0.15821.443444.974218.1815
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1LA1 - 1071 - 112
2X-RAY DIFFRACTION2LA108 - 213113 - 215
3X-RAY DIFFRACTION3HB1 - 1131 - 131
4X-RAY DIFFRACTION3PC305 - 3191 - 13
5X-RAY DIFFRACTION4HB114 - 227132 - 231
6X-RAY DIFFRACTION5MD1 - 1071 - 112
7X-RAY DIFFRACTION6MD108 - 213113 - 215
8X-RAY DIFFRACTION7IE1 - 1131 - 131
9X-RAY DIFFRACTION7QF305 - 3191 - 13
10X-RAY DIFFRACTION8IE114 - 227132 - 231

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