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- PDB-1rzi: Crystal structure of human anti-HIV-1 gp120-reactive antibody 47e fab -

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Basic information

Entry
Database: PDB / ID: 1rzi
TitleCrystal structure of human anti-HIV-1 gp120-reactive antibody 47e fab
Components
  • Fab 47e heavy chain
  • Fab 47e light chain
KeywordsIMMUNE SYSTEM / HIV-1 / gp120 / CD4i / antibodies / tyrosine sulfation / VH-gene usage
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsHuang, C.C. / Venturi, M. / Majeed, S. / Moore, M.J. / Phogat, S. / Zhang, M.-Y. / Dimitrov, D.S. / Hendrickson, W.A. / Robinson, J. / Sodroski, J. ...Huang, C.C. / Venturi, M. / Majeed, S. / Moore, M.J. / Phogat, S. / Zhang, M.-Y. / Dimitrov, D.S. / Hendrickson, W.A. / Robinson, J. / Sodroski, J. / Wyatt, R. / Choe, H. / Farzan, M. / Kwong, P.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Structural basis of tyrosine sulfation and VH-gene usage in antibodies that recognize the HIV type 1 coreceptor-binding site on gp120
Authors: Huang, C.C. / Venturi, M. / Majeed, S. / Moore, M.J. / Phogat, S. / Zhang, M.-Y. / Dimitrov, D.S. / Hendrickson, W.A. / Robinson, J. / Sodroski, J. / Wyatt, R. / Choe, H. / Farzan, M. / Kwong, P.D.
History
DepositionDec 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
A: Fab 47e light chain
B: Fab 47e heavy chain
C: Fab 47e light chain
D: Fab 47e heavy chain
E: Fab 47e light chain
F: Fab 47e heavy chain
G: Fab 47e light chain
H: Fab 47e heavy chain
I: Fab 47e light chain
J: Fab 47e heavy chain
K: Fab 47e light chain
L: Fab 47e heavy chain
M: Fab 47e light chain
N: Fab 47e heavy chain
O: Fab 47e light chain
P: Fab 47e heavy chain


Theoretical massNumber of molelcules
Total (without water)378,59716
Polymers378,59716
Non-polymers00
Water7,044391
1
A: Fab 47e light chain
B: Fab 47e heavy chain


Theoretical massNumber of molelcules
Total (without water)47,3252
Polymers47,3252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-21 kcal/mol
Surface area19000 Å2
MethodPISA
2
C: Fab 47e light chain
D: Fab 47e heavy chain


Theoretical massNumber of molelcules
Total (without water)47,3252
Polymers47,3252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-22 kcal/mol
Surface area19470 Å2
MethodPISA
3
E: Fab 47e light chain
F: Fab 47e heavy chain


Theoretical massNumber of molelcules
Total (without water)47,3252
Polymers47,3252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-23 kcal/mol
Surface area19520 Å2
MethodPISA
4
G: Fab 47e light chain
H: Fab 47e heavy chain


Theoretical massNumber of molelcules
Total (without water)47,3252
Polymers47,3252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-22 kcal/mol
Surface area19260 Å2
MethodPISA
5
I: Fab 47e light chain
J: Fab 47e heavy chain


Theoretical massNumber of molelcules
Total (without water)47,3252
Polymers47,3252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-22 kcal/mol
Surface area19040 Å2
MethodPISA
6
K: Fab 47e light chain
L: Fab 47e heavy chain


Theoretical massNumber of molelcules
Total (without water)47,3252
Polymers47,3252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-20 kcal/mol
Surface area19430 Å2
MethodPISA
7
M: Fab 47e light chain
N: Fab 47e heavy chain


Theoretical massNumber of molelcules
Total (without water)47,3252
Polymers47,3252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-20 kcal/mol
Surface area19380 Å2
MethodPISA
8
O: Fab 47e light chain
P: Fab 47e heavy chain


Theoretical massNumber of molelcules
Total (without water)47,3252
Polymers47,3252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-23 kcal/mol
Surface area18890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.430, 111.645, 133.309
Angle α, β, γ (deg.)85.48, 90.00, 89.71
Int Tables number1
Cell settingtriclinic
Space group name H-MP1

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Components

#1: Antibody
Fab 47e light chain


Mass: 23166.619 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Genus (production host): Lymphocryptovirus
Cell (production host): IMMORTALIZED B-CELL CLONE FUSED WITH A MURINE B-CELL FUSION PARTNER
Production host: Human herpesvirus 4 (Epstein-Barr virus)
#2: Antibody
Fab 47e heavy chain


Mass: 24157.945 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Genus (production host): Lymphocryptovirus
Cell (production host): IMMORTALIZED B-CELL CLONE FUSED WITH A MURINE B-CELL FUSION PARTNER
Production host: Human herpesvirus 4 (Epstein-Barr virus)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 58.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 1.2M ammonium citrate, 0.1M Tris-HCl, 4% PEG1000, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
12.5 mMTris-HCl1drop
20.35 M1dropNaCl
30.02 %(v/v)1dropNaN3pH7.0
44-8 mg/mlprotein1drop
51.2 Mammonium citrate1reservoir
60.1 MTris-HCl1reservoir
74 %PEG10001reservoirpH9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 12, 2003
RadiationMonochromator: Si (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 84392 / Observed criterion σ(I): -3 / Biso Wilson estimate: 64.3 Å2
Reflection shellResolution: 2.8→2.91 Å / % possible all: 31.1
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 30 Å / % possible obs: 81.9 % / Num. measured all: 390048 / Rmerge(I) obs: 0.176
Reflection shell
*PLUS
% possible obs: 31.1 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 257118.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.321 7671 10.1 %RANDOM
Rwork0.233 ---
all0.2331 ---
obs0.2331 76315 81.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.3048 Å2 / ksol: 0.267058 e/Å3
Displacement parametersBiso mean: 57.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.11 Å23.04 Å20 Å2
2--19.17 Å2-7.27 Å2
3----17.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.59 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.75 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25582 0 0 391 25973
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it2.282
X-RAY DIFFRACTIONc_scbond_it1.672
X-RAY DIFFRACTIONc_scangle_it2.542.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.457 658 9.9 %
Rwork0.386 6011 -
obs--43 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.319 / Rfactor Rwork: 0.231
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0087
X-RAY DIFFRACTIONc_angle_deg1.569
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.1

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