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- PDB-1e4w: crossreactive binding of a circularized peptide to an anti-TGFalp... -

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Basic information

Entry
Database: PDB / ID: 1e4w
Titlecrossreactive binding of a circularized peptide to an anti-TGFalpha antibody Fab-fragment
Components
  • (TAB2) x 2
  • CYCLIC PEPTIDE
KeywordsIMMUNE SYSTEM / COMPLEX (ANTIBODY-ANTIGEN) / CROSS-REACTIVITY / PROTEIN-PEPTIDE RECOGNITION
Function / homology
Function and homology information


positive regulation of B cell activation / phagocytosis, recognition / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin complex, circulating / phagocytosis, engulfment / endosome to lysosome transport ...positive regulation of B cell activation / phagocytosis, recognition / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin complex, circulating / phagocytosis, engulfment / endosome to lysosome transport / antigen processing and presentation / immunoglobulin mediated immune response / regulation of proteolysis / positive regulation of endocytosis / complement activation, classical pathway / antigen binding / multivesicular body / positive regulation of phagocytosis / B cell differentiation / response to bacterium / positive regulation of immune response / extracellular region / plasma membrane
Similarity search - Function
: / 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 / Immunoglobulin-like fold ...: / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / Immunoglobulin kappa constant / Immunoglobulin heavy constant gamma 2A
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHahn, M. / Winkler, D. / Misselwitz, R. / Wessner, H. / Welfle, K. / Zahn, G. / Schneider-Mergener, J. / Hoehne, W.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Cross-Reactive Binding of Cyclic Peptides to an Anti-Tgf Alpha Antibody Fab Fragment: An X-Ray Structural and Thermodynamic Analysis
Authors: Hahn, M. / Winkler, D. / Welfle, K. / Misselwitz, R. / Welfle, H. / Wessner, H. / Zahn, G. / Scholz, C. / Seifert, M. / Harkins, R. / Schneider-Mergener, J. / Hoehne, W.
History
DepositionJul 12, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2019Group: Data collection / Other / Source and taxonomy / Category: pdbx_database_status / pdbx_entity_src_syn / Item: _pdbx_database_status.status_code_sf
Revision 1.4Dec 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 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: TAB2
L: TAB2
P: CYCLIC PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4835
Polymers47,3883
Non-polymers942
Water7,368409
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-37.6 kcal/mol
Surface area24000 Å2
MethodPQS
Unit cell
Length a, b, c (Å)49.220, 94.350, 121.790
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/peptide , 1 types, 1 molecules P

#3: Protein/peptide CYCLIC PEPTIDE


Mass: 925.918 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Antibody , 2 types, 2 molecules HL

#1: Antibody TAB2


Mass: 22884.605 Da / Num. of mol.: 1 / Fragment: IG KAPPA HEAVY CHAIN / Source method: isolated from a natural source / Details: MURINE FAB-FRAGMENT / Source: (natural) MUS MUSCULUS (house mouse) / Cell line: MOUSE HYBRIDOMA / Organ: SPLEEN / References: UniProt: P01865*PLUS
#2: Antibody TAB2


Mass: 23577.947 Da / Num. of mol.: 1 / Fragment: IG KAPPA LIGHT CHAIN / Source method: isolated from a natural source / Details: MURINE FAB-FRAGMENT / Source: (natural) MUS MUSCULUS (house mouse) / Cell line: MOUSE HYBRIDOMA / Organ: SPLEEN / Strain: BALB/C / References: UniProt: P01837*PLUS

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Non-polymers , 3 types, 411 molecules

#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCHAIN P IS A CIRCULAR CLOSED HEPTAMER OF THE SEQUENCE SER-HIS-PHE-ASN-GLU-TYR-GLU. THE N-ATOM OF ...CHAIN P IS A CIRCULAR CLOSED HEPTAMER OF THE SEQUENCE SER-HIS-PHE-ASN-GLU-TYR-GLU. THE N-ATOM OF SER-1 IS COVALENTLY CONNECTED WITH CD OF GLU-7. CHAIN L: THE C-TERMINAL REGION IS THE CONSTANT REGION OF THE IG KAPPA LIGHT CHAIN, THE N-TERMINAL REGION IS THE VARIABLE REGION OF THE IG KAPPA LIGHT CHAIN THE VARIABLE REGION IS AUTOANTIBODY REACTIVE WITH SPECTRIN, (4-HYRDOXY-3-NITROPHENYL) ACETYL, AND FLUORESCEIN, WHICH PROMOTES CENTRAL NERVOUS SYSTEM REMYELINATION
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: 51.1 %
Crystal growpH: 8.5
Details: PROTEIN IN TRIS-HCL, 8.5 11-14 MG/ML PRECIPITANT: 12% PEG MME 2000, 5 MM NICL2, 0.1 M TRIS-HCL, PH 8.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
112 %PEG2000 MME1reservoir
25 mM1reservoirNiCl2
30.1 MTris-HCl1reservoirpH8.5
411-14 mg/mlprotein1drop
520 mMTris-HCl1droppH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.3
DetectorType: XRAY RESEARCH / Detector: CCD / Date: Jun 17, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 1.95→74.5 Å / Num. obs: 39968 / % possible obs: 94.6 % / Redundancy: 9.9 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 19.5
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 5.7 / % possible all: 54.2
Reflection shell
*PLUS
% possible obs: 54.2 % / Mean I/σ(I) obs: 6.5

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FBI

1fbi


Resolution: 1.95→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.269 2099 5 %RANDOM
Rwork0.204 ---
obs-41695 94.6 %-
Displacement parametersBiso mean: 35.9 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3331 0 2 409 3742
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0240.02
X-RAY DIFFRACTIONp_angle_d0.0450.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0660.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.5082
X-RAY DIFFRACTIONp_mcangle_it3.3173
X-RAY DIFFRACTIONp_scbond_it3.1482
X-RAY DIFFRACTIONp_scangle_it4.3783
X-RAY DIFFRACTIONp_plane_restr0.0284
X-RAY DIFFRACTIONp_chiral_restr0.2880.15
X-RAY DIFFRACTIONp_singtor_nbd0.1880.3
X-RAY DIFFRACTIONp_multtor_nbd0.2590.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor8.27
X-RAY DIFFRACTIONp_staggered_tor18.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor21.620
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_bond_d / Dev ideal: 0.016

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