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

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Basic information

Entry
Database: PDB / ID: 5mwf
TitleHuman Jagged2 C2-EGF2
ComponentsProtein jagged-2
KeywordsSIGNALING PROTEIN / C2 / EGF / Notch
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 / von Willebrand factor (vWF) type C domain / EGF-like, conserved site ...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 / von Willebrand factor (vWF) type C domain / EGF-like, conserved site / Human growth factor-like EGF / 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: 2.8 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 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 / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
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.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_struct_assembly_gen.asym_id_list / _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 / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein jagged-2
B: Protein jagged-2
C: Protein jagged-2
D: Protein jagged-2
E: Protein jagged-2
F: Protein jagged-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,98231
Polymers195,3206
Non-polymers4,66225
Water4,179232
1
A: Protein jagged-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4426
Polymers32,5531
Non-polymers8885
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein jagged-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4426
Polymers32,5531
Non-polymers8885
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein jagged-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4065
Polymers32,5531
Non-polymers8534
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protein jagged-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2445
Polymers32,5531
Non-polymers6914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Protein jagged-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2445
Polymers32,5531
Non-polymers6914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Protein jagged-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2044
Polymers32,5531
Non-polymers6513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.628, 92.929, 97.004
Angle α, β, γ (deg.)71.68, 83.16, 82.68
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Protein jagged-2 / hJ2 / Jagged-2


Mass: 32553.395 Da / Num. of mol.: 6
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

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Sugars , 2 types, 6 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 251 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.71 Å3/Da / Density % sol: 54.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: PEG 8000, Ammonium sulphate, Sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.93 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.8→38.009 Å / Num. obs: 49334 / % possible obs: 97.6 % / Redundancy: 2.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.103 / Net I/σ(I): 7.3
Reflection shellResolution: 2.8→2.89 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.685 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.58 / % possible all: 97.7

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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: 5MW5

5mw5


Resolution: 2.8→38.009 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 29.66
RfactorNum. reflection% reflection
Rfree0.2751 2392 4.85 %
Rwork0.2172 --
obs0.22 49334 97.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→38.009 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12370 0 280 232 12882
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01313164
X-RAY DIFFRACTIONf_angle_d0.75517765
X-RAY DIFFRACTIONf_dihedral_angle_d16.4637734
X-RAY DIFFRACTIONf_chiral_restr0.0481809
X-RAY DIFFRACTIONf_plane_restr0.0062315
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.85720.4541470.37072765X-RAY DIFFRACTION98
2.8572-2.91930.43481360.34282747X-RAY DIFFRACTION97
2.9193-2.98720.39661560.31322755X-RAY DIFFRACTION97
2.9872-3.06180.35221590.27712693X-RAY DIFFRACTION98
3.0618-3.14460.29311480.26912769X-RAY DIFFRACTION97
3.1446-3.23710.34721360.2592778X-RAY DIFFRACTION98
3.2371-3.34150.34741400.2642797X-RAY DIFFRACTION98
3.3415-3.46080.32171540.25192776X-RAY DIFFRACTION98
3.4608-3.59930.27381310.24292721X-RAY DIFFRACTION97
3.5993-3.7630.3151450.2132742X-RAY DIFFRACTION97
3.763-3.96120.28151280.20292776X-RAY DIFFRACTION98
3.9612-4.20910.24381320.1832800X-RAY DIFFRACTION98
4.2091-4.53360.20031270.16522762X-RAY DIFFRACTION98
4.5336-4.98890.22151390.16162758X-RAY DIFFRACTION98
4.9889-5.70870.21251240.17882794X-RAY DIFFRACTION97
5.7087-7.18440.24411480.20342759X-RAY DIFFRACTION98
7.1844-38.01240.21271420.1942750X-RAY DIFFRACTION97

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