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- PDB-3ru8: Structure of an HIV epitope scaffold in complex with neutralizing... -

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Basic information

Entry
Database: PDB / ID: 3ru8
TitleStructure of an HIV epitope scaffold in complex with neutralizing antibody b12 Fab
Components
  • Antibody b12, Heavy Chain
  • Antibody b12, Light Chain
  • Epitope Scaffold 2bodx43
KeywordsDE NOVO PROTEIN / IMMUNE SYSTEM / binding epitope from HIV on a heterologous 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 / 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 / antigen binding / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / 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 / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
1, 4-beta cellobiohydrolase / : / 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 ...1, 4-beta cellobiohydrolase / : / 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 / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Immunoglobulin kappa constant
Similarity search - Component
Biological speciesHuman immunodeficiency virus
synthetic construct (others)
Thermomonospora fusca (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.07 Å
AuthorsCarrico, C.T.D. / Strong, R.K.
CitationJournal: Science / Year: 2011
Title: Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold.
Authors: Azoitei, M.L. / Correia, B.E. / Ban, Y.E. / Carrico, C. / Kalyuzhniy, O. / Chen, L. / Schroeter, A. / Huang, P.S. / McLellan, J.S. / Kwong, P.D. / Baker, D. / Strong, R.K. / Schief, W.R.
History
DepositionMay 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Epitope Scaffold 2bodx43
H: Antibody b12, Heavy Chain
L: Antibody b12, Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0587
Polymers78,6903
Non-polymers3684
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-31 kcal/mol
Surface area29470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.453, 93.097, 94.373
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Epitope Scaffold 2bodx43


Mass: 30043.268 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus, synthetic construct, Thermomonospora fusca
Plasmid: pET29 / Production host: Escherichia coli (E. coli)
#2: Antibody Antibody b12, Heavy Chain


Mass: 24938.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Antibody b12, Light Chain


Mass: 23707.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: P01834*PLUS
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsEPITOPE SCAFFOLD 2BODX43 INCORPORATES A SMALL SECTION OF HIV-1 GP120 INTO A PROTEIN FROM ...EPITOPE SCAFFOLD 2BODX43 INCORPORATES A SMALL SECTION OF HIV-1 GP120 INTO A PROTEIN FROM THERMOMONOSPORA FUSCA, PLUS SOME DESIGNED REGIONS NATIVE TO NEITHER ORGANISM. THE CLOSER MATCH WITH THE CRYSTALLIZED SEQUENCE OF THIS CHAIN CORRESPONDS TO UNP ENTRY P26222.

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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: 2.52 Å3/Da / Density % sol: 51.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 18% PEG-3350, 0.22M potassium nitrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. obs: 49114 / % possible obs: 99.7 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.103 / Χ2: 3.009 / Net I/σ(I): 12.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.07-2.115.20.3423110.882195.3
2.11-2.145.90.31124260.9291100
2.14-2.195.90.27524111.0591100
2.19-2.235.90.24824341.1331100
2.23-2.285.90.23624421.2351100
2.28-2.335.90.21824361.2861100
2.33-2.395.90.19624281.4091100
2.39-2.455.90.17924571.5171100
2.45-2.535.90.1724141.6571100
2.53-2.615.90.15424511.9131100
2.61-2.75.90.1424472.2231100
2.7-2.815.90.13124532.7121100
2.81-2.945.90.11724453.1911100
2.94-3.095.90.11124673.804199.9
3.09-3.295.90.10224614.5081100
3.29-3.545.80.09324745.553199.9
3.54-3.95.80.0924876.8441100
3.9-4.465.80.08725098.125199.9
4.46-5.625.60.06825155.714199.4
5.62-505.50.05226464.189198.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 43.67 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å45.23 Å
Translation2.5 Å45.23 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 2BOD, 2NY7

2bod

2ny7


Resolution: 2.07→45.23 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.1955 / WRfactor Rwork: 0.1631 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8875 / SU B: 7.774 / SU ML: 0.097 / SU R Cruickshank DPI: 0.1793 / SU Rfree: 0.1521 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2026 2485 5.1 %RANDOM
Rwork0.1678 ---
obs0.1696 48971 99.25 %-
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 max: 111.05 Å2 / Biso mean: 40.2672 Å2 / Biso min: 3.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2---0.03 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.07→45.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5372 0 24 343 5739
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225699
X-RAY DIFFRACTIONr_bond_other_d0.0010.023806
X-RAY DIFFRACTIONr_angle_refined_deg1.1661.9397805
X-RAY DIFFRACTIONr_angle_other_deg0.80539294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9065763
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.89823.796245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58815857
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3921536
X-RAY DIFFRACTIONr_chiral_restr0.0720.2853
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216527
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021170
X-RAY DIFFRACTIONr_mcbond_it0.71823638
X-RAY DIFFRACTIONr_mcbond_other0.1721468
X-RAY DIFFRACTIONr_mcangle_it1.3335873
X-RAY DIFFRACTIONr_scbond_it2.02142061
X-RAY DIFFRACTIONr_scangle_it3.1261905
LS refinement shellResolution: 2.069→2.123 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.208 178 -
Rwork0.176 3201 -
all-3379 -
obs--94.57 %
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)
11.56360.78610.03272.2081-0.91861.1706-0.0030.0290.13260.1677-0.01430.0664-0.1501-0.07890.01730.08620.02320.02220.16210.00690.122-5.0856-0.6088-22.3595
21.91760.49840.14251.5674-0.38941.3872-0.04440.0747-0.2822-0.0593-0.0702-0.29140.11070.06340.11470.08950.00810.05250.17850.02290.22441.2868-14.4141-23.5758
31.2028-0.2201-0.3760.83510.16183.50720.05490.00150.06110.0110.1120.0579-0.1527-0.1412-0.16690.0910.00230.05090.17810.0230.2063-19.3226-18.29034.6533
47.7299-0.79741.27781.30820.30052.3186-0.0308-0.30030.35620.0352-0.0188-0.1248-0.2343-0.0310.04960.08010.01220.02480.1261-0.07310.0944.1547-17.709831.8394
52.1458-0.6036-0.17231.82770.22962.7152-0.05550.0102-0.08250.07440.1442-0.02550.05460.0707-0.08870.0712-0.0020.02310.1427-0.02410.1353-5.5924-34.68710.334
62.1741-0.7838-3.0121.58443.54479.7496-0.1639-0.3017-0.14790.49510.05540.06740.98340.24910.10850.19590.0741-0.00340.1919-0.00470.07693.4869-33.507734.4232
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1X1 - 140
2X-RAY DIFFRACTION2X141 - 277
3X-RAY DIFFRACTION3H1 - 126
4X-RAY DIFFRACTION4H127 - 227
5X-RAY DIFFRACTION5L1 - 107
6X-RAY DIFFRACTION6L108 - 213

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