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- PDB-4cc1: Notch ligand, Jagged-1, contains an N-terminal C2 domain -

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Basic information

Entry
Database: PDB / ID: 4cc1
TitleNotch ligand, Jagged-1, contains an N-terminal C2 domain
ComponentsPROTEIN JAGGED-1
KeywordsSIGNALING PROTEIN / GLYCOPROTEIN / EXTRACELLULAR / DEVELOPMENTAL PROTEIN / NOTCH SIGNALING PATHWAY / EGF / DSL / LIPID / NOTCH / MEMBRANE / PROTEIN-BINDING / TRANSMEMBRANE / EGF-LIKE DOMAIN / DISEASE MUTATION
Function / homology
Function and homology information


endocardial cushion cell development / loop of Henle development / ciliary body morphogenesis / Nephron development / regulation of reproductive process / pulmonary artery morphogenesis / cardiac neural crest cell development involved in outflow tract morphogenesis / podocyte development / negative regulation of endothelial cell differentiation / morphogenesis of an epithelial sheet ...endocardial cushion cell development / loop of Henle development / ciliary body morphogenesis / Nephron development / regulation of reproductive process / pulmonary artery morphogenesis / cardiac neural crest cell development involved in outflow tract morphogenesis / podocyte development / negative regulation of endothelial cell differentiation / morphogenesis of an epithelial sheet / nephron development / positive regulation of myeloid cell differentiation / cardiac right ventricle morphogenesis / inhibition of neuroepithelial cell differentiation / distal tubule development / neuroendocrine cell differentiation / aorta morphogenesis / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / T cell mediated immunity / positive regulation of cardiac epithelial to mesenchymal transition / NOTCH4 Activation and Transmission of Signal to the Nucleus / inner ear auditory receptor cell differentiation / endothelial cell differentiation / neuronal stem cell population maintenance / pulmonary valve morphogenesis / cell fate determination / negative regulation of stem cell differentiation / regulation of epithelial cell proliferation / aortic valve morphogenesis / myoblast differentiation / Notch binding / RUNX3 regulates NOTCH signaling / negative regulation of cell-matrix adhesion / negative regulation of cell-cell adhesion / negative regulation of fat cell differentiation / positive regulation of Notch signaling pathway / cardiac septum morphogenesis / response to muramyl dipeptide / hemopoiesis / negative regulation of neuron differentiation / RAC3 GTPase cycle / blood vessel remodeling / positive regulation of osteoblast differentiation / keratinocyte differentiation / Notch signaling pathway / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / RAC1 GTPase cycle / Activated NOTCH1 Transmits Signal to the Nucleus / negative regulation of cell migration / NOTCH3 Activation and Transmission of Signal to the Nucleus / adherens junction / growth factor activity / phospholipid binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / nervous system development / regulation of cell population proliferation / angiogenesis / molecular adaptor activity / apical plasma membrane / calcium ion binding / structural molecule activity / positive regulation of transcription by RNA polymerase II / extracellular region / membrane / plasma membrane
Similarity search - Function
Immunoglobulin-like - #3510 / 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 ...Immunoglobulin-like - #3510 / 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 / : / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-L-fucopyranose / Protein jagged-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsChilakuri, C.R. / Sheppard, D. / Ilagan, M.X.G. / Holt, L.R. / Abbott, F. / Liang, S. / Kopan, R. / Handford, P.A. / Lea, S.M.
CitationJournal: Cell Rep. / Year: 2013
Title: Structural Analysis Uncovers Lipid-Binding Properties of Notch Ligands
Authors: Chilakuri, C.R. / Sheppard, D. / Ilagan, M.X.G. / Holt, L.R. / Abbott, F. / Liang, S. / Kopan, R. / Handford, P.A. / Lea, S.M.
History
DepositionOct 17, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Dec 25, 2013Group: Atomic model
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _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_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.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.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 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: PROTEIN JAGGED-1
B: PROTEIN JAGGED-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,65115
Polymers69,6282
Non-polymers1,02413
Water1086
1
A: PROTEIN JAGGED-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3818
Polymers34,8141
Non-polymers5677
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROTEIN JAGGED-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2707
Polymers34,8141
Non-polymers4566
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.950, 60.560, 63.030
Angle α, β, γ (deg.)92.89, 104.95, 105.92
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.3, -0.597, 0.744), (-0.591, -0.496, -0.636), (0.749, -0.631, -0.204)
Vector: -28.36608, 11.95355, -15.59484)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PROTEIN JAGGED-1 / JAGGED1 / HJ1 / CD339


Mass: 34813.750 Da / Num. of mol.: 2 / Fragment: RESIDUES 32-335
Source method: isolated from a genetically manipulated source
Details: NAG LINKAGE AT N217 IN BOTH A, B CHAINS, FUC LINKAGE AT T311 IN A CHAIN
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK 293S / Production host: HOMO SAPIENS (human) / References: UniProt: P78504

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Sugars , 2 types, 3 molecules

#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.: 2
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: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose / Fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 16 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.47 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.84→60.38 Å / Num. obs: 17793 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 2.45 % / Biso Wilson estimate: 91.13 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 11.3

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Processing

SoftwareName: BUSTER / Version: 2.11.4 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VJ2

2vj2


Resolution: 2.84→60.38 Å / Cor.coef. Fo:Fc: 0.9121 / Cor.coef. Fo:Fc free: 0.8577 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.354
RfactorNum. reflection% reflectionSelection details
Rfree0.2493 988 5.59 %RANDOM
Rwork0.1963 ---
obs0.1991 17666 98.22 %-
Displacement parametersBiso mean: 68.42 Å2
Baniso -1Baniso -2Baniso -3
1-5.8415 Å2-8.1611 Å2-11.2776 Å2
2---10.6196 Å21.9217 Å2
3---4.7781 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.84→60.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4726 0 54 6 4786
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014939HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.236715HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1671SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes142HARMONIC2
X-RAY DIFFRACTIONt_gen_planes722HARMONIC5
X-RAY DIFFRACTIONt_it4939HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion20.55
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion607SEMIHARMONIC5
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_contact5064SEMIHARMONIC4
LS refinement shellResolution: 2.84→3.01 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.3468 162 5.78 %
Rwork0.273 2639 -
all0.2773 2801 -
obs--98.22 %

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