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- PDB-5veb: Crystal structure of a Fab binding to extracellular domain 5 of C... -

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Basic information

Entry
Database: PDB / ID: 5veb
TitleCrystal structure of a Fab binding to extracellular domain 5 of Cadherin-6
Components
  • (anti-CDH6 Fab heavy ...) x 2
  • Cadherin-6
  • anti-CDH6 Fab light chain
KeywordsIMMUNE SYSTEM / antibody / cell adhesion / antibody-drug conjugate / cancer
Function / homology
Function and homology information


IgD immunoglobulin complex / IgM immunoglobulin complex / multicellular organism development / IgA immunoglobulin complex / IgE immunoglobulin complex / cell-cell adhesion via plasma-membrane adhesion molecules / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / CD22 mediated BCR regulation / Adherens junctions interactions / catenin complex ...IgD immunoglobulin complex / IgM immunoglobulin complex / multicellular organism development / IgA immunoglobulin complex / IgE immunoglobulin complex / cell-cell adhesion via plasma-membrane adhesion molecules / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / CD22 mediated BCR regulation / Adherens junctions interactions / catenin complex / cell-cell junction assembly / Fc epsilon receptor (FCERI) signaling / adherens junction organization / immunoglobulin complex / Classical antibody-mediated complement activation / IgG immunoglobulin complex / Initial triggering of complement / homophilic cell adhesion via plasma membrane adhesion molecules / FCGR activation / immunoglobulin mediated immune response / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / Notch signaling pathway / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / antigen binding / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / adherens junction / B cell receptor signaling pathway / cell morphogenesis / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell junction / adaptive immune response / Potential therapeutics for SARS / blood microparticle / membrane => GO:0016020 / cell adhesion / cadherin binding / immune response / calcium ion binding / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like ...Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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 / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-galactopyranose / Immunoglobulin kappa constant / Cadherin-6 / IgG H chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.34 Å
AuthorsZhu, X. / Bialucha, C.U. / London, A. / Clark, K. / Hu, T.
CitationJournal: Cancer Discov / Year: 2017
Title: Discovery and Optimization of HKT288, a Cadherin-6-Targeting ADC for the Treatment of Ovarian and Renal Cancers.
Authors: Bialucha, C.U. / Collins, S.D. / Li, X. / Saxena, P. / Zhang, X. / Durr, C. / Lafont, B. / Prieur, P. / Shim, Y. / Mosher, R. / Lee, D. / Ostrom, L. / Hu, T. / Bilic, S. / Rajlic, I.L. / ...Authors: Bialucha, C.U. / Collins, S.D. / Li, X. / Saxena, P. / Zhang, X. / Durr, C. / Lafont, B. / Prieur, P. / Shim, Y. / Mosher, R. / Lee, D. / Ostrom, L. / Hu, T. / Bilic, S. / Rajlic, I.L. / Capka, V. / Jiang, W. / Wagner, J.P. / Elliott, G. / Veloso, A. / Piel, J.C. / Flaherty, M.M. / Mansfield, K.G. / Meseck, E.K. / Rubic-Schneider, T. / London, A.S. / Tschantz, W.R. / Kurz, M. / Nguyen, D. / Bourret, A. / Meyer, M.J. / Faris, J.E. / Janatpour, M.J. / Chan, V.W. / Yoder, N.C. / Catcott, K.C. / McShea, M.A. / Sun, X. / Gao, H. / Williams, J. / Hofmann, F. / Engelman, J.A. / Ettenberg, S.A. / Sellers, W.R. / Lees, E.
History
DepositionApr 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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_validate_close_contact / struct_conn / 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_validate_close_contact.auth_atom_id_2 / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Apr 24, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / entity_src_nat / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_asym / struct_conn / struct_ref / struct_ref_seq
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _entity_name_com.entity_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.entity_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _struct_ref_seq.ref_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: anti-CDH6 Fab heavy chain
B: anti-CDH6 Fab light chain
H: anti-CDH6 Fab heavy chain
L: anti-CDH6 Fab light chain
X: Cadherin-6
Y: Cadherin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,00910
Polymers122,1256
Non-polymers8854
Water4,342241
1
A: anti-CDH6 Fab heavy chain
B: anti-CDH6 Fab light chain
X: Cadherin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5545
Polymers61,1123
Non-polymers4422
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6890 Å2
ΔGint-26 kcal/mol
Surface area23320 Å2
MethodPISA
2
H: anti-CDH6 Fab heavy chain
L: anti-CDH6 Fab light chain
Y: Cadherin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4555
Polymers61,0133
Non-polymers4422
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-26 kcal/mol
Surface area23590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.829, 88.855, 186.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 3 types, 4 molecules ABLH

#1: Antibody anti-CDH6 Fab heavy chain


Mass: 23823.510 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: S6B291
#2: Antibody anti-CDH6 Fab light chain


Mass: 23380.926 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01834
#3: Antibody anti-CDH6 Fab heavy chain


Mass: 23724.443 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: S6B291, UniProt: P55285*PLUS

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Protein / Sugars / Non-polymers , 3 types, 247 molecules XY

#4: Protein Cadherin-6 / / Kidney cadherin / K-cadherin


Mass: 13907.368 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDH6 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P55285
#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.: 4
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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.68 Å3/Da / Density % sol: 54.1 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG3350, 0.2M di-ammonium hydrogen citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.34→80.23 Å / Num. obs: 55887 / % possible obs: 99.5 % / Redundancy: 6.4 % / Biso Wilson estimate: 47.86 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 17.3
Reflection shellResolution: 2.34→2.348 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 535 / % possible all: 100

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Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTERrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementResolution: 2.34→80.23 Å / Cor.coef. Fo:Fc: 0.9347 / Cor.coef. Fo:Fc free: 0.903 / SU R Cruickshank DPI: 0.312 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.313 / SU Rfree Blow DPI: 0.229 / SU Rfree Cruickshank DPI: 0.231
RfactorNum. reflection% reflectionSelection details
Rfree0.2523 2824 5.08 %RANDOM
Rwork0.2124 ---
obs0.2144 55641 99.09 %-
Displacement parametersBiso max: 144.19 Å2 / Biso mean: 40.61 Å2 / Biso min: 8.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.2752 Å20 Å20 Å2
2--4.7345 Å20 Å2
3----5.0097 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: final / Resolution: 2.34→80.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8193 0 63 241 8497
Biso mean--61.7 35.69 -
Num. residues----1084
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2775SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes192HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1265HARMONIC5
X-RAY DIFFRACTIONt_it8451HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1136SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9186SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8451HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg11486HARMONIC21.24
X-RAY DIFFRACTIONt_omega_torsion3.6
X-RAY DIFFRACTIONt_other_torsion19.27
LS refinement shellResolution: 2.34→2.4 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2903 205 5.03 %
Rwork0.2282 3868 -
all0.2312 4073 -
obs--99.09 %

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