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- PDB-3h3p: Crystal structure of HIV epitope-scaffold 4E10 Fv complex -

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Basic information

Entry
Database: PDB / ID: 3h3p
TitleCrystal structure of HIV epitope-scaffold 4E10 Fv complex
Components
  • 4E10_S0_1TJLC_004_N
  • Fv 4E10 heavy chain
  • Fv 4E10 light chain
KeywordsIMMUNE SYSTEM / epitope-scaffold Fv complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
artificial gene (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHolmes, M.A.
CitationJournal: J.Virol. / Year: 2010
Title: Interactions between lipids and human anti-HIV antibody 4E10 can be reduced without ablating neutralizing activity
Authors: Xu, H. / Song, L. / Kim, M. / Holmes, M.A. / Kraft, Z. / Sellhorn, G. / Reinherz, E.L. / Stamatatos, L. / Strong, R.K.
History
DepositionApr 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fv 4E10 heavy chain
I: Fv 4E10 heavy chain
L: Fv 4E10 light chain
M: Fv 4E10 light chain
S: 4E10_S0_1TJLC_004_N
T: 4E10_S0_1TJLC_004_N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0777
Polymers75,0376
Non-polymers401
Water99155
1
H: Fv 4E10 heavy chain
L: Fv 4E10 light chain
S: 4E10_S0_1TJLC_004_N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5594
Polymers37,5193
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-30 kcal/mol
Surface area11270 Å2
MethodPISA
2
I: Fv 4E10 heavy chain
M: Fv 4E10 light chain
T: 4E10_S0_1TJLC_004_N


Theoretical massNumber of molelcules
Total (without water)37,5193
Polymers37,5193
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.400, 92.400, 272.790
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Antibody Fv 4E10 heavy chain


Mass: 14712.454 Da / Num. of mol.: 2 / Mutation: W104A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL
#2: Antibody Fv 4E10 light chain


Mass: 12304.698 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL
#3: Protein 4E10_S0_1TJLC_004_N


Mass: 10501.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The author states that THE EPITOPE-SCAFFOLD IS BASED on transcription factor DksA from E. coli (PDB ID 1TJL).
Source: (gene. exp.) artificial gene (others) / Plasmid: pET29 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) star
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsFV HEAVY CHAIN CONTAINS A REMNANT OF SINGLE-CHAIN LINKER AT N-TERMINUS GS. FV LIGHT CHAIN CONTAINS ...FV HEAVY CHAIN CONTAINS A REMNANT OF SINGLE-CHAIN LINKER AT N-TERMINUS GS. FV LIGHT CHAIN CONTAINS A REMNANT OF SINGLE-CHAIN LINKER AT C-TERMINUS KLVPR. FV HEAVY CHAIN HAS BEEN MUTATED TO ALA AT POSITION 104 (KABAT POSITION 100)

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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: 2.24 Å3/Da / Density % sol: 45.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M calcium acetate, 8% PEG 8000, 0.1 M Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 107 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 13, 2008 / Details: Rigaku VariMax HR
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→69.02 Å / Num. all: 19557 / Num. obs: 19557 / % possible obs: 98.6 % / Redundancy: 4.56 % / Biso Wilson estimate: 63.6 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 7.5
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.29 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 2.9 / Num. unique all: 8305 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.2.0019refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: computationally-derived model of the Fv, based on 1TZG

1tzg


Resolution: 2.7→60.08 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.896 / SU B: 25.371 / SU ML: 0.26 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic, 1 tls group per chain / Cross valid method: THROUGHOUT / ESU R: 0.725 / ESU R Free: 0.364 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28697 953 4.9 %RANDOM
Rwork0.2289 ---
obs0.23171 18347 97.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 59.2 Å2
Refinement stepCycle: LAST / Resolution: 2.7→60.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3794 0 1 55 3850
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223881
X-RAY DIFFRACTIONr_bond_other_d0.0070.022583
X-RAY DIFFRACTIONr_angle_refined_deg1.1091.9475284
X-RAY DIFFRACTIONr_angle_other_deg0.7223.0036267
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6465502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.99923.377151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.59715572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8681524
X-RAY DIFFRACTIONr_chiral_restr0.0610.2592
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024379
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02805
X-RAY DIFFRACTIONr_nbd_refined0.2360.3616
X-RAY DIFFRACTIONr_nbd_other0.2270.32506
X-RAY DIFFRACTIONr_nbtor_refined0.1910.51810
X-RAY DIFFRACTIONr_nbtor_other0.0880.52166
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.5218
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1220.53
X-RAY DIFFRACTIONr_metal_ion_refined0.0770.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.33
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2420.318
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.51
X-RAY DIFFRACTIONr_mcbond_it0.722566
X-RAY DIFFRACTIONr_mcbond_other0.09421041
X-RAY DIFFRACTIONr_mcangle_it1.04834012
X-RAY DIFFRACTIONr_scbond_it1.61141530
X-RAY DIFFRACTIONr_scangle_it2.42161272
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 64 -
Rwork0.254 1351 -
obs--99.44 %
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)
12.9008-0.6475-0.42242.7051-0.68162.63350.0018-0.09010.0068-0.0373-0.0273-0.1044-0.1325-0.03730.02550.1356-0.00560.02520.2484-0.03710.2433-0.671-31.816-7.313
21.5029-0.469-0.26141.16440.46372.48250.04540.0368-0.04850.11240.02310.03010.04150.1441-0.06850.1880.01530.04930.2652-0.01030.2375-22.511-26.6910.61
33.677-0.1961-0.39382.96190.63873.98870.0206-0.43490.78870.1892-0.0014-0.3158-0.77540.1466-0.01920.2091-0.0998-0.06230.2694-0.09910.386412.995-19.1063.031
41.9202-0.0392-0.36951.8813-0.78665.8854-0.02510.07550.1291-0.34850.05890.0901-0.4447-0.194-0.03380.17710.06190.02790.2183-0.00810.2971-39.486-15.826-8.078
53.2248-1.68780.58238.4697-3.984711.00780.23910.39770.3967-0.6586-0.362-0.7414-0.4921.0290.12290.1934-0.0067-0.02050.18350.04450.29838.191-21.05-21.25
613.887212.31255.265814.2741.16499.43770.0171-0.53611.12030.6698-0.49170.2708-1.37080.30980.47460.2859-0.06940.06930.215-0.04540.307-22.877-8.82714.747
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 127
2X-RAY DIFFRACTION2I1 - 128
3X-RAY DIFFRACTION3L1 - 109
4X-RAY DIFFRACTION4M1 - 111
5X-RAY DIFFRACTION5S44 - 61
6X-RAY DIFFRACTION6T44 - 64

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