[English] 日本語
Yorodumi
- PDB-7abv: Structure of the S1-cleaved mouse Notch1 Negative Regulatory Regi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7abv
TitleStructure of the S1-cleaved mouse Notch1 Negative Regulatory Region (NRR)
ComponentsNeurogenic locus notch homolog protein 1
KeywordsSIGNALING PROTEIN / Type I transmembrane protein / Developmental protein / Calcium binding
Function / homology
Function and homology information


Pre-NOTCH Processing in Golgi / cardiac right ventricle formation / regulation of inner ear auditory receptor cell differentiation / negative regulation of inner ear auditory receptor cell differentiation / positive regulation of aorta morphogenesis / apoptotic process involved in embryonic digit morphogenesis / osteoblast fate commitment / negative regulation of photoreceptor cell differentiation / venous blood vessel morphogenesis / regulation of somitogenesis ...Pre-NOTCH Processing in Golgi / cardiac right ventricle formation / regulation of inner ear auditory receptor cell differentiation / negative regulation of inner ear auditory receptor cell differentiation / positive regulation of aorta morphogenesis / apoptotic process involved in embryonic digit morphogenesis / osteoblast fate commitment / negative regulation of photoreceptor cell differentiation / venous blood vessel morphogenesis / regulation of somitogenesis / foregut morphogenesis / regulation of epithelial cell proliferation involved in prostate gland development / positive regulation of ephrin receptor signaling pathway / positive regulation of glial cell differentiation / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / CSL-Notch-Mastermind transcription factor complex / auditory receptor cell fate commitment / compartment pattern specification / coronary sinus valve morphogenesis / cardiac right atrium morphogenesis / growth involved in heart morphogenesis / regulation of cardioblast proliferation / mesenchymal cell development / cell differentiation in spinal cord / venous endothelial cell differentiation / endocardial cushion development / arterial endothelial cell differentiation / collecting duct development / cell migration involved in endocardial cushion formation / negative regulation of pro-B cell differentiation / mitral valve formation / : / endocardium morphogenesis / somatic stem cell division / distal tubule development / MAML1-RBP-Jkappa- ICN1 complex / prostate gland epithelium morphogenesis / cardiac chamber formation / cardiac atrium morphogenesis / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling / negative regulation of endothelial cell chemotaxis / atrioventricular node development / cardiac ventricle morphogenesis / positive regulation of transcription of Notch receptor target / pericardium morphogenesis / cellular response to tumor cell / Activated NOTCH1 Transmits Signal to the Nucleus / Notch-HLH transcription pathway / positive regulation of smooth muscle cell differentiation / endoderm development / glomerular mesangial cell development / vasculogenesis involved in coronary vascular morphogenesis / negative regulation of extracellular matrix constituent secretion / regulation of extracellular matrix assembly / positive regulation of apoptotic process involved in morphogenesis / chemical synaptic transmission, postsynaptic / endocardial cell differentiation / epithelial to mesenchymal transition involved in endocardial cushion formation / left/right axis specification / T-helper 17 type immune response / positive regulation of endothelial cell differentiation / cardiac left ventricle morphogenesis / coronary vein morphogenesis / negative regulation of myotube differentiation / cardiac vascular smooth muscle cell development / embryonic hindlimb morphogenesis / endocardium development / neuronal stem cell population maintenance / positive regulation of astrocyte differentiation / negative regulation of cell adhesion molecule production / cardiac muscle cell myoblast differentiation / tissue regeneration / negative regulation of calcium ion-dependent exocytosis / positive regulation of cardiac epithelial to mesenchymal transition / regulation of Notch signaling pathway / negative regulation of oligodendrocyte differentiation / cardiac epithelial to mesenchymal transition / heart trabecula morphogenesis / regulation of cell adhesion involved in heart morphogenesis / interleukin-17-mediated signaling pathway / neuron fate commitment / negative regulation of catalytic activity / negative regulation of myoblast differentiation / negative regulation of collagen biosynthetic process / cellular response to follicle-stimulating hormone stimulus / glial cell differentiation / camera-type eye morphogenesis / negative regulation of cardiac muscle hypertrophy / negative regulation of stem cell differentiation / luteolysis / pulmonary valve morphogenesis / tube formation / determination of left/right symmetry / regulation of epithelial cell proliferation / cardiac muscle tissue morphogenesis / embryonic limb morphogenesis / positive regulation of keratinocyte differentiation / inflammatory response to antigenic stimulus / coronary artery morphogenesis
Similarity search - Function
Neurogenic locus notch homolog protein 1 / Notch, C-terminal / Domain of unknown function / : / Notch / Notch, NOD domain / Notch, NODP domain / NOTCH protein / NOTCH protein / NOD ...Neurogenic locus notch homolog protein 1 / 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 1. / EGF-like domain signature 2. / EGF-like domain / Ankyrin repeat profile. / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
Neurogenic locus notch homolog protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.065 Å
AuthorsZeronian, M.R. / Janssen, B.J.C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Notch-Jagged signaling complex defined by an interaction mosaic.
Authors: Zeronian, M.R. / Klykov, O. / Portell I de Montserrat, J. / Konijnenberg, M.J. / Gaur, A. / Scheltema, R.A. / Janssen, B.J.C.
History
DepositionSep 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 4, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Neurogenic locus notch homolog protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0616
Polymers31,4981
Non-polymers5635
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint6 kcal/mol
Surface area11960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.724, 65.724, 161.683
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-3176-

HOH

-
Components

#1: Protein Neurogenic locus notch homolog protein 1 / Notch 1 / Motch A / mT14 / p300


Mass: 31497.936 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Notch1, Motch / Production host: Homo sapiens (human) / References: UniProt: Q01705
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 2.0 M sodium chloride, 0.1 M sodium acetate pH 4.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.06998 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06998 Å / Relative weight: 1
ReflectionResolution: 2.065→60.886 Å / Num. obs: 15144 / % possible obs: 91.5 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.03 / Rrim(I) all: 0.109 / Net I/σ(I): 14.6
Reflection shellResolution: 2.065→2.296 Å / Redundancy: 11.8 % / Rmerge(I) obs: 1.431 / Num. unique obs: 757 / CC1/2: 0.77 / Rpim(I) all: 0.43 / Rrim(I) all: 1.496 / % possible all: 64.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
MOLREPphasing
STARANISOdata scaling
Aimlessdata scaling
XDSdata reduction
autoPROCdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ETO

3eto


Resolution: 2.065→60.885 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.932 / Cross valid method: THROUGHOUT / ESU R: 0.251 / ESU R Free: 0.208
RfactorNum. reflection% reflection
Rfree0.2375 795 5.25 %
Rwork0.196 14348 -
all0.198 --
obs-15143 66.922 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 57.792 Å2
Baniso -1Baniso -2Baniso -3
1--0.597 Å20 Å20 Å2
2---0.597 Å2-0 Å2
3---1.194 Å2
Refinement stepCycle: LAST / Resolution: 2.065→60.885 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1796 0 31 77 1904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0121877
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.6432557
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3895230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.7424.857105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.26815283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.636156
X-RAY DIFFRACTIONr_chiral_restr0.1040.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021483
X-RAY DIFFRACTIONr_nbd_refined0.2350.2889
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21305
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2106
X-RAY DIFFRACTIONr_metal_ion_refined0.1290.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.20.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1490.27
X-RAY DIFFRACTIONr_mcbond_it1.6233.144926
X-RAY DIFFRACTIONr_mcangle_it2.724.7061154
X-RAY DIFFRACTIONr_scbond_it2.1963.424948
X-RAY DIFFRACTIONr_scangle_it3.4615.0581400
X-RAY DIFFRACTIONr_lrange_it6.21844.1482880
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.065-2.1190.19940.306940.30116440.8330.8275.96110.3
2.119-2.1770.363150.2811740.28815750.8670.862120.276
2.177-2.240.31120.2842430.28515410.8660.85316.54770.276
2.24-2.3080.278180.2552880.25715010.8490.88820.38640.246
2.308-2.3840.251370.2645870.26314610.8680.87942.71050.246
2.384-2.4680.306410.2537600.25614200.8430.89456.40850.225
2.468-2.5610.279570.2610950.26113800.8730.8883.47830.236
2.561-2.6650.3590.24712610.2513330.8840.88799.02480.223
2.665-2.7830.287650.2411970.24212620.9030.8971000.209
2.783-2.9190.265670.21111590.21412260.9150.9241000.186
2.919-3.0760.234670.20110960.20311640.9140.93599.91410.178
3.076-3.2620.25630.21210440.21411070.9130.9361000.193
3.262-3.4870.226500.1949970.19510470.9340.9531000.178
3.487-3.7650.191450.1877680.1879820.9480.96282.79020.175
3.765-4.1230.19340.1566870.1589130.9590.9778.97040.153
4.123-4.6070.213530.1617740.1648270.9560.9661000.161
4.607-5.3140.248290.1757160.1787450.9460.9591000.181
5.314-6.4970.238370.1926060.1956430.9290.9531000.199
6.497-9.1360.262260.1734940.1775210.9460.9699.80810.193
9.136-60.8850.225160.2013070.2033290.9510.95998.17630.238
Refinement TLS params.Method: refined / Origin x: 1.9 Å / Origin y: 17.619 Å / Origin z: -21.405 Å
111213212223313233
T0.3832 Å2-0.0061 Å20.0541 Å2-0.0562 Å2-0.0428 Å2--0.0636 Å2
L2.7443 °20.9533 °2-1.3979 °2-2.6715 °2-1.3213 °2--2.3221 °2
S-0.1845 Å °0.239 Å °-0.3285 Å °-0.7653 Å °0.1718 Å °-0.1435 Å °0.3315 Å °-0.0202 Å °0.0127 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA1448 - 1717
2X-RAY DIFFRACTION1ALLAaA3001
3X-RAY DIFFRACTION1ALLAbA3002
4X-RAY DIFFRACTION1ALLAcA3003
5X-RAY DIFFRACTION1ALLAdA3004

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more