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- PDB-3iet: Crystal Structure of 237mAb with antigen -

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Basic information

Entry
Database: PDB / ID: 3iet
TitleCrystal Structure of 237mAb with antigen
Components
  • (Immunoglobulin ...Antibody) x 2
  • PodoplaninPDPN
KeywordsIMMUNE SYSTEM / glycopepitde / antibody / Fab / carbohydrate-biding / tumour
Function / homology
Function and homology information


tube morphogenesis / lymphatic endothelial cell fate commitment / regulation of myofibroblast contraction / actin-mediated cell contraction / GPVI-mediated activation cascade / visceral serous pericardium development / leading edge of lamellipodium / lymphangiogenesis / regulation of substrate adhesion-dependent cell spreading / positive regulation of extracellular matrix disassembly ...tube morphogenesis / lymphatic endothelial cell fate commitment / regulation of myofibroblast contraction / actin-mediated cell contraction / GPVI-mediated activation cascade / visceral serous pericardium development / leading edge of lamellipodium / lymphangiogenesis / regulation of substrate adhesion-dependent cell spreading / positive regulation of extracellular matrix disassembly / chemokine binding / regulation of lamellipodium morphogenesis / tetraspanin-enriched microdomain / positive regulation of platelet aggregation / positive regulation of platelet activation / filopodium membrane / anchoring junction / positive regulation of cell motility / wound healing, spreading of cells / microvillus membrane / lung alveolus development / prostaglandin metabolic process / regulation of G1/S transition of mitotic cell cycle / lamellipodium membrane / Rho protein signal transduction / response to hyperoxia / positive regulation of epithelial to mesenchymal transition / lymph node development / regulation of cell adhesion / ruffle / filopodium / cell projection / lung development / cell-cell adhesion / ruffle membrane / cell migration / lamellipodium / cell junction / regulation of cell shape / protein-folding chaperone binding / cytoplasmic vesicle / basolateral plasma membrane / cell population proliferation / membrane => GO:0016020 / cell adhesion / positive regulation of cell migration / membrane raft / apical plasma membrane / negative regulation of cell population proliferation / external side of plasma membrane / signaling receptor binding / negative regulation of apoptotic process / signal transduction / mitochondrion / membrane / plasma membrane / cytosol
Similarity search - Function
Podoplanin / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-galactopyranose / Podoplanin / Podoplanin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBrooks, C.L. / Evans, S.V. / Borisova, S.N.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Antibody recognition of a unique tumor-specific glycopeptide antigen.
Authors: Brooks, C.L. / Schietinger, A. / Borisova, S.N. / Kufer, P. / Okon, M. / Hirama, T. / Mackenzie, C.R. / Wang, L.X. / Schreiber, H. / Evans, S.V.
#1: Journal: Science / Year: 2006
Title: A mutant chaperone converts a wild-type protein into a tumor-specific antien
Authors: Schietinger, A. / Philip, M. / Yoshida, B.A. / Azadi, P. / Liu, H. / Meredith, S.C. / Schreiber, H.
History
DepositionJul 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Immunoglobulin light chain (IgG2a)
B: Immunoglobulin heavy chain (IgG2a)
C: Immunoglobulin light chain (IgG2a)
D: Immunoglobulin heavy chain (IgG2a)
X: Podoplanin
Q: Podoplanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,39612
Polymers96,6926
Non-polymers7046
Water9,386521
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Immunoglobulin light chain (IgG2a)
B: Immunoglobulin heavy chain (IgG2a)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4924
Polymers47,3622
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-25 kcal/mol
Surface area18990 Å2
MethodPISA
3
C: Immunoglobulin light chain (IgG2a)
D: Immunoglobulin heavy chain (IgG2a)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4924
Polymers47,3622
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-23 kcal/mol
Surface area19380 Å2
MethodPISA
4
X: Podoplanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,2052
Polymers9841
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
Q: Podoplanin
hetero molecules


  • defined by software
  • 1.21 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,2052
Polymers9841
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)277.910, 38.240, 95.910
Angle α, β, γ (deg.)90.00, 108.99, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Antibody , 2 types, 4 molecules ACBD

#1: Antibody Immunoglobulin light chain (IgG2a)


Mass: 23823.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/c / Production host: Mus musculus (house mouse)
#2: Antibody Immunoglobulin heavy chain (IgG2a)


Mass: 23538.295 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)

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Protein/peptide / Sugars , 2 types, 4 molecules XQ

#3: Protein/peptide Podoplanin / PDPN


Mass: 984.123 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pdpn, RP23-348F1.2-002 / Production host: Mus musculus (house mouse) / References: UniProt: A8Y5F6, UniProt: Q62011*PLUS
#5: Sugar ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE / N-Acetylgalactosamine


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 525 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 521 / Source method: isolated from a natural source / Formula: H2O

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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: 2.48 Å3/Da / Density % sol: 50.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG MME 5000, ZnCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002+ / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 13, 2007 / Details: mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→19.86 Å / Num. obs: 48616 / % possible obs: 98.5 % / Redundancy: 7.96 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obs% possible all
2.2-2.288.160.3284.899.7
2.28-2.378.210.314.999.7
2.37-2.488.150.2625.699.7
2.48-2.618.050.2186.399.4
2.61-2.777.990.1688.199.1
2.77-2.987.840.11511.198.4
2.98-3.287.750.07914.997.6
3.28-3.767.650.05420.796.1
3.76-4.727.720.04324.695.9
4.72-19.868.040.04225.799.5

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Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata processing
PHENIX1.4_4refinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M71

1m71


Resolution: 2.2→19.86 Å / Occupancy max: 1 / Occupancy min: 0.35 / SU ML: 0.88 / σ(F): 1.34 / Phase error: 28.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2712 2433 5.03 %
Rwork0.227 --
obs0.2293 48352 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.301 Å2 / ksol: 0.377 e/Å3
Displacement parametersBiso mean: 37.633 Å2
Baniso -1Baniso -2Baniso -3
1--1.844 Å20 Å2-1.415 Å2
2--7.569 Å2-0 Å2
3----5.725 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6651 0 32 521 7204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066843
X-RAY DIFFRACTIONf_angle_d1.1879292
X-RAY DIFFRACTIONf_dihedral_angle_d19.0112440
X-RAY DIFFRACTIONf_chiral_restr0.0891051
X-RAY DIFFRACTIONf_plane_restr0.0051182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.24490.34181560.26072737X-RAY DIFFRACTION99
2.2449-2.29360.32231190.24672674X-RAY DIFFRACTION100
2.2936-2.34690.3241350.25252745X-RAY DIFFRACTION99
2.3469-2.40550.30051580.24472722X-RAY DIFFRACTION99
2.4055-2.47040.31971520.24362643X-RAY DIFFRACTION99
2.4704-2.54290.35461360.26282779X-RAY DIFFRACTION99
2.5429-2.62480.33251360.25922661X-RAY DIFFRACTION99
2.6248-2.71840.32311600.25912739X-RAY DIFFRACTION99
2.7184-2.8270.31181270.25972647X-RAY DIFFRACTION98
2.827-2.95520.28821430.24362716X-RAY DIFFRACTION98
2.9552-3.11050.25071450.2382662X-RAY DIFFRACTION97
3.1105-3.30450.27661290.21642656X-RAY DIFFRACTION96
3.3045-3.55840.27311370.20682620X-RAY DIFFRACTION95
3.5584-3.9140.22921520.19372613X-RAY DIFFRACTION95
3.914-4.47470.2131320.17422638X-RAY DIFFRACTION95
4.4747-5.61640.20031470.18122778X-RAY DIFFRACTION98
5.6164-19.86440.27591690.25272889X-RAY DIFFRACTION99

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