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- PDB-3lev: HIV-1 antibody 2F5 in complex with epitope scaffold ES2 -

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Basic information

Entry
Database: PDB / ID: 3lev
TitleHIV-1 antibody 2F5 in complex with epitope scaffold ES2
Components
  • (2F5 ANTIBODY ...) x 2
  • RNA polymerase sigma factor
KeywordsIMMUNE SYSTEM / HIV-1 / GP41 / MONOCLONAL ANTIBODY / 2F5 / SCAFFOLD / EPITOPE / TRANSPLANT / GRAFT / SIGMA FACTOR / RE-ELICITATION / VACCINE DESIGN
Function / homology
Function and homology information


sigma factor activity / DNA-templated transcription initiation / DNA binding / cytoplasm
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1810 / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / : / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 ...Four Helix Bundle (Hemerythrin (Met), subunit A) - #1810 / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / : / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / Four Helix Bundle (Hemerythrin (Met), subunit A) / Winged helix-like DNA-binding domain superfamily / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / RNA polymerase sigma factor SigA
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsOfek, G. / Guenaga, F.J. / Schief, W.R. / Skinner, J. / Baker, D. / Wyatt, R. / Kwong, P.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Elicitation of structure-specific antibodies by epitope scaffolds.
Authors: Ofek, G. / Guenaga, F.J. / Schief, W.R. / Skinner, J. / Baker, D. / Wyatt, R. / Kwong, P.D.
History
DepositionJan 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 31, 2021Group: Derived calculations / Source and taxonomy / Category: entity_src_gen / struct_site
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 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
A: RNA polymerase sigma factor
L: 2F5 ANTIBODY LIGHT CHAIN
H: 2F5 ANTIBODY HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5826
Polymers68,7453
Non-polymers8383
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: RNA polymerase sigma factor


Theoretical massNumber of molelcules
Total (without water)20,2091
Polymers20,2091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
L: 2F5 ANTIBODY LIGHT CHAIN
H: 2F5 ANTIBODY HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3735
Polymers48,5362
Non-polymers8383
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-26 kcal/mol
Surface area20270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.506, 63.933, 200.019
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein RNA polymerase sigma factor


Mass: 20209.309 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 93-271
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: SIGMA FACTOR SIGA / Plasmid: CMV-R / Cell line (production host): HEK293F / Production host: HOMO SAPIENS (human) / References: UniProt: Q9EZJ8

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Antibody , 2 types, 2 molecules LH

#2: Antibody 2F5 ANTIBODY LIGHT CHAIN


Mass: 23305.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: HETEROMYELOMA CELL LINE FUSED WITH PERIPHERAL BLOOD MONONUCLEAR CELLS
Cell line (production host): CB-F7 / Production host: HOMO SAPIENS (human)
#3: Antibody 2F5 ANTIBODY HEAVY CHAIN


Mass: 25229.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: HETEROMYELOMA CELL LINE FUSED WITH PERIPHERAL BLOOD MONONUCLEAR CELLS
Cell line (production host): CB-F7 / Production host: HOMO SAPIENS (human)

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Non-polymers , 4 types, 100 molecules

#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.72 Å3/Da / Density % sol: 54.79 %
Crystal growpH: 5.5
Details: 16% PEG 400, 2.8% PEG 3350, 0.1 M CH3COONA PH 5.5, 0.02 M ATP, VAPOR DIFFUSION, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 9, 2007
RadiationMonochromator: SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 23675 / % possible obs: 88.9 % / Observed criterion σ(I): 5 / Redundancy: 8.9 % / Biso Wilson estimate: 69.4 Å2 / Rsym value: 0.09 / Net I/σ(I): 42.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.17 / Rsym value: 0.47 / % possible all: 33.1

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1KU2 AND 1TJI

1ku2

1tji


Resolution: 2.5→46.15 Å / SU ML: 0.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.253 2222 9.9 %
Rwork0.201 --
obs0.206 22446 84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 94.15 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 106.86 Å2
Baniso -1Baniso -2Baniso -3
1-3.0943 Å20 Å2-0 Å2
2--2.5165 Å2-0 Å2
3----9.5441 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4821 0 53 97 4971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075014
X-RAY DIFFRACTIONf_angle_d0.9596811
X-RAY DIFFRACTIONf_dihedral_angle_d15.2791835
X-RAY DIFFRACTIONf_chiral_restr0.053776
X-RAY DIFFRACTIONf_plane_restr0.005858
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)
12.61550.9037-0.6144-0.89770.7732.0618-0.1726-0.56421.9781-0.5040.6727-0.2869-0.50380.1366-0.12390.61070.0942-0.08070.4543-0.49911.50921.9597-21.655810.1007
22.5132-0.42641.08891.05660.06881.21040.1969-0.55341.5225-0.3279-0.0905-0.2641-1.5696-0.08170.44311.1732-0.2968-0.19020.6549-0.40771.78798.9658-12.928218.8628
31.84811.18-0.40390.8819-0.66090.31490.5995-0.05212.46420.149-0.11970.67370.34150.176-0.23490.8535-0.01130.10770.6437-0.52161.9813-4.7255-23.36386.5074
40.9375-0.02910.1416-1.2182-0.13850.03430.095-0.5130.62730.25930.0490.8028-0.044-0.0733-0.2110.93150.04270.32980.6752-0.11891.617-11.9163-27.857812.1719
51.68380.47650.63551.1373-0.89972.9559-0.20080.47770.23140.02950.0967-0.1801-0.23970.74240.09420.3485-0.1275-0.0480.57320.02830.469916.0368-39.1503-15.813
62.1336-0.1379-1.99194.19540.07910.9550.04450.2498-0.0614-0.88660.2089-0.4738-0.118-0.1452-0.19050.7515-0.08050.14750.6579-0.00350.54629.6012-45.1336-51.6364
71.4008-0.395-0.82910.53790.3592.4914-0.0644-0.03220.05980.0983-0.01950.02420.0956-0.05930.05850.30240.03890.00430.25470.0370.2974-4.2902-45.9963-14.7003
80.92570.45460.6531.77031.04392.1302-0.1338-0.1855-0.18260.10520.1524-0.22630.4965-0.566-0.03580.63650.08350.04570.42750.0460.39994.9096-57.612-43.2639
92.01311.4431-1.39150.758-0.41921.9590.78820.27380.48190.0316-0.2048-0.2167-0.761-0.7126-0.35671.127-0.11580.16571.22970.22850.9329-12.1476-20.5957-11.1649
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 93:158
2X-RAY DIFFRACTION2chain A and resid 159:186
3X-RAY DIFFRACTION3chain A and resid 187:225
4X-RAY DIFFRACTION4chain A and resid 226:271
5X-RAY DIFFRACTION5chain L and resid 1:111
6X-RAY DIFFRACTION6chain L and resid 112:214
7X-RAY DIFFRACTION7chain H and resid 1:128
8X-RAY DIFFRACTION8chain H and resid 129:237
9X-RAY DIFFRACTION9chain N

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