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- PDB-5mw5: Human Jagged2 C2-EGF2 -

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Basic information

Entry
Database: PDB / ID: 5mw5
TitleHuman Jagged2 C2-EGF2
ComponentsProtein jagged-2
KeywordsSIGNALING PROTEIN / C2 / EGF / Notch / signaling
Function / homology
Function and homology information


epithelial cell apoptotic process involved in palatal shelf morphogenesis / thymic T cell selection / auditory receptor cell fate commitment / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / respiratory system process / morphogenesis of embryonic epithelium / gamma-delta T cell differentiation / Notch binding / positive regulation of Notch signaling pathway / odontogenesis of dentin-containing tooth ...epithelial cell apoptotic process involved in palatal shelf morphogenesis / thymic T cell selection / auditory receptor cell fate commitment / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / respiratory system process / morphogenesis of embryonic epithelium / gamma-delta T cell differentiation / Notch binding / positive regulation of Notch signaling pathway / odontogenesis of dentin-containing tooth / T cell differentiation / regulation of cell adhesion / Notch signaling pathway / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / skeletal system development / NOTCH3 Activation and Transmission of Signal to the Nucleus / growth factor activity / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / regulation of cell population proliferation / spermatogenesis / in utero embryonic development / cell differentiation / calcium ion binding / plasma membrane
Similarity search - Function
Jagged/Serrate protein / Delta-like/Jagged, EGF-like domain / Delta/Serrate/lag-2 (DSL) protein / Notch ligand, N-terminal domain / Delta serrate ligand / N terminus of Notch ligand C2-like domain / DSL domain profile. / delta serrate ligand / EGF-like, conserved site / Human growth factor-like EGF ...Jagged/Serrate protein / Delta-like/Jagged, EGF-like domain / Delta/Serrate/lag-2 (DSL) protein / Notch ligand, N-terminal domain / Delta serrate ligand / N terminus of Notch ligand C2-like domain / DSL domain profile. / delta serrate ligand / EGF-like, conserved site / Human growth factor-like EGF / von Willebrand factor (vWF) type C domain / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / Calcium-binding EGF domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSuckling, R.J. / Handford, P.A. / Lea, S.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/L001187/1 United Kingdom
CitationJournal: EMBO J. / Year: 2017
Title: Structural and functional dissection of the interplay between lipid and Notch binding by human Notch ligands.
Authors: Suckling, R.J. / Korona, B. / Whiteman, P. / Chillakuri, C. / Holt, L. / Handford, P.A. / Lea, S.M.
History
DepositionJan 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...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: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 1.4Jan 17, 2024Group: 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

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Assembly

Deposited unit
A: Protein jagged-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8955
Polymers32,5531
Non-polymers3414
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint-36 kcal/mol
Surface area15870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.266, 83.878, 99.352
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein jagged-2 / hJ2


Mass: 32553.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JAG2 / Plasmid: pEXS2-2 / Cell (production host): Schneider 2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q9Y219
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 3.09 Å3/Da / Density % sol: 60.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: PEG 8000, potassium dihydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.3 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 2.7→83.9 Å / Num. obs: 11513 / % possible obs: 99.6 % / Redundancy: 7.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.107 / Net I/σ(I): 12.9
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 3.7 / CC1/2: 0.892 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MV7

5mv7


Resolution: 2.7→64.091 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.62
RfactorNum. reflection% reflection
Rfree0.2635 578 5.02 %
Rwork0.2299 --
obs0.2315 11513 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 55.6 Å2
Refinement stepCycle: LAST / Resolution: 2.7→64.091 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2016 0 17 43 2076
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062117
X-RAY DIFFRACTIONf_angle_d0.6862859
X-RAY DIFFRACTIONf_dihedral_angle_d18.9141239
X-RAY DIFFRACTIONf_chiral_restr0.043286
X-RAY DIFFRACTIONf_plane_restr0.004375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.97180.34231340.29632675X-RAY DIFFRACTION100
2.9718-3.40180.32841400.25672704X-RAY DIFFRACTION100
3.4018-4.28570.24191600.21442711X-RAY DIFFRACTION99
4.2857-64.10950.23751440.21282845X-RAY DIFFRACTION99

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