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- PDB-5mwb: Human Notch-2 EGF11-13 -

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Basic information

Entry
Database: PDB / ID: 5mwb
TitleHuman Notch-2 EGF11-13
ComponentsNeurogenic locus notch homolog protein 2
KeywordsSIGNALING PROTEIN / EGF / Notch / receptor / signaling
Function / homology
Function and homology information


cholangiocyte proliferation / proximal tubule development / regulation of osteoclast development / intrahepatic bile duct development / glomerular capillary formation / ciliary body morphogenesis / podocyte development / Defective LFNG causes SCDO3 / morphogenesis of an epithelial sheet / marginal zone B cell differentiation ...cholangiocyte proliferation / proximal tubule development / regulation of osteoclast development / intrahepatic bile duct development / glomerular capillary formation / ciliary body morphogenesis / podocyte development / Defective LFNG causes SCDO3 / morphogenesis of an epithelial sheet / marginal zone B cell differentiation / Pre-NOTCH Processing in the Endoplasmic Reticulum / atrioventricular node development / cellular response to tumor cell / positive regulation of keratinocyte proliferation / atrial septum morphogenesis / positive regulation of smooth muscle cell differentiation / hepatocyte proliferation / left/right axis specification / NOTCH2 intracellular domain regulates transcription / Pre-NOTCH Processing in Golgi / placenta blood vessel development / myeloid dendritic cell differentiation / pulmonary valve morphogenesis / bone remodeling / cell fate determination / positive regulation of BMP signaling pathway / positive regulation of osteoclast differentiation / inflammatory response to antigenic stimulus / positive regulation of Ras protein signal transduction / Notch binding / embryonic limb morphogenesis / NOTCH4 Intracellular Domain Regulates Transcription / Notch-HLH transcription pathway / heart looping / humoral immune response / hemopoiesis / NF-kappaB binding / cis-regulatory region sequence-specific DNA binding / BMP signaling pathway / Notch signaling pathway / NOTCH2 Activation and Transmission of Signal to the Nucleus / animal organ morphogenesis / axon guidance / wound healing / multicellular organism growth / Pre-NOTCH Transcription and Translation / cilium / positive regulation of miRNA transcription / nervous system development / signaling receptor activity / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / positive regulation of ERK1 and ERK2 cascade / receptor complex / intracellular signal transduction / defense response to bacterium / positive regulation of apoptotic process / Golgi membrane / negative regulation of gene expression / apoptotic process / calcium ion binding / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / negative regulation of transcription by RNA polymerase II / cell surface / positive regulation of transcription by RNA polymerase II / extracellular region / nucleoplasm / membrane / nucleus / plasma membrane
Similarity search - Function
Neurogenic locus notch homolog protein 2 / Notch, C-terminal / Domain of unknown function / Notch / Notch, NOD domain / Notch, NODP domain / NOTCH protein / NOTCH protein / NOD / NODP ...Neurogenic locus notch homolog protein 2 / Notch, C-terminal / Domain of unknown function / Notch / Notch, NOD domain / Notch, NODP domain / NOTCH protein / NOTCH protein / NOD / NODP / Notch-like domain superfamily / LNR (Lin-12/Notch) repeat profile. / LNR domain / Notch domain / Domain found in Notch and Lin-12 / EGF-like, conserved site / Human growth factor-like EGF / : / Calcium-binding EGF domain / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / 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. / Ankyrin repeat / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
beta-D-glucopyranose / alpha-L-fucopyranose / Neurogenic locus notch homolog protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 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 / 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_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_atom_id ..._atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_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: Neurogenic locus notch homolog protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9227
Polymers17,1451
Non-polymers7776
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint3 kcal/mol
Surface area8060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)20.160, 49.790, 125.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Neurogenic locus notch homolog protein 2 / hN2


Mass: 17145.312 Da / Num. of mol.: 1 / Fragment: UNP residues 414-532
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NOTCH2 / Plasmid: pEXS2-2 / Cell (production host): Schneider 2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q04721

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Sugars , 3 types, 3 molecules

#2: Polysaccharide beta-D-xylopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 312.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpb1-3DGlcpb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a212h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Xylp]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-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
#4: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 124 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 1.84 Å3/Da / Density % sol: 33.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: PEG 8000, Sodium acetate, Sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.86→41.8 Å / Num. obs: 11247 / % possible obs: 99.5 % / Redundancy: 5.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Net I/σ(I): 11.2
Reflection shellResolution: 1.86→1.91 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.067 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.524 / % possible all: 99.3

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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: 2VJ3

2vj3


Resolution: 1.86→39.003 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.94
RfactorNum. reflection% reflection
Rfree0.2636 574 5.1 %
Rwork0.2278 --
obs0.2298 11247 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.86→39.003 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms872 0 44 121 1037
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021970
X-RAY DIFFRACTIONf_angle_d0.551296
X-RAY DIFFRACTIONf_dihedral_angle_d14.583585
X-RAY DIFFRACTIONf_chiral_restr0.043143
X-RAY DIFFRACTIONf_plane_restr0.003171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8602-2.04740.40151300.32242608X-RAY DIFFRACTION99
2.0474-2.34370.33231350.27092612X-RAY DIFFRACTION100
2.3437-2.95260.30891460.26182667X-RAY DIFFRACTION99
2.9526-39.0120.221630.19312786X-RAY DIFFRACTION99

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