[English] 日本語
Yorodumi
- PDB-5czx: Crystal structure of Notch3 NRR in complex with 20358 Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5czx
TitleCrystal structure of Notch3 NRR in complex with 20358 Fab
Components
  • 20358 Fab heavy chain
  • 20358 Fab light chain
  • Neurogenic locus notch homolog protein 3
KeywordsIMMUNE SYSTEM / ANTIBODY / NOTCH3 / ONCOLOGY
Function / homology
Function and homology information


glomerular capillary formation / Defective LFNG causes SCDO3 / Pre-NOTCH Processing in the Endoplasmic Reticulum / Noncanonical activation of NOTCH3 / neuroblast differentiation / Pre-NOTCH Processing in Golgi / neuron fate commitment / Notch binding / NOTCH3 Intracellular Domain Regulates Transcription / artery morphogenesis ...glomerular capillary formation / Defective LFNG causes SCDO3 / Pre-NOTCH Processing in the Endoplasmic Reticulum / Noncanonical activation of NOTCH3 / neuroblast differentiation / Pre-NOTCH Processing in Golgi / neuron fate commitment / Notch binding / NOTCH3 Intracellular Domain Regulates Transcription / artery morphogenesis / Notch-HLH transcription pathway / negative regulation of neuron differentiation / forebrain development / Notch signaling pathway / NOTCH3 Activation and Transmission of Signal to the Nucleus / positive regulation of smooth muscle cell proliferation / axon guidance / Pre-NOTCH Transcription and Translation / positive regulation of miRNA transcription / signaling receptor activity / receptor complex / cadherin binding / Golgi membrane / calcium ion binding / endoplasmic reticulum membrane / enzyme binding / negative regulation of transcription by RNA polymerase II / cell surface / positive regulation of transcription by RNA polymerase II / extracellular region / nucleoplasm / identical protein binding / plasma membrane / cytosol
Similarity search - Function
GMP Synthetase; Chain A, domain 3 - #320 / Alpha-Beta Plaits - #3310 / Neurogenic locus Notch 3 / Notch, C-terminal / Domain of unknown function / Notch / Notch, NOD domain / Notch, NODP domain / NOTCH protein / NOTCH protein ...GMP Synthetase; Chain A, domain 3 - #320 / Alpha-Beta Plaits - #3310 / Neurogenic locus Notch 3 / 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 / Ankyrin repeats (many copies) / GMP Synthetase; Chain A, domain 3 / 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 / Alpha-Beta Plaits / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Neurogenic locus notch homolog protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHu, T. / Fryer, C. / Chopra, R. / Clark, K.
CitationJournal: Oncogene / Year: 2016
Title: Characterization of activating mutations of NOTCH3 in T-cell acute lymphoblastic leukemia and anti-leukemic activity of NOTCH3 inhibitory antibodies.
Authors: Bernasconi-Elias, P. / Hu, T. / Jenkins, D. / Firestone, B. / Gans, S. / Kurth, E. / Capodieci, P. / Deplazes-Lauber, J. / Petropoulos, K. / Thiel, P. / Ponsel, D. / Hee Choi, S. / LeMotte, ...Authors: Bernasconi-Elias, P. / Hu, T. / Jenkins, D. / Firestone, B. / Gans, S. / Kurth, E. / Capodieci, P. / Deplazes-Lauber, J. / Petropoulos, K. / Thiel, P. / Ponsel, D. / Hee Choi, S. / LeMotte, P. / London, A. / Goetcshkes, M. / Nolin, E. / Jones, M.D. / Slocum, K. / Kluk, M.J. / Weinstock, D.M. / Christodoulou, A. / Weinberg, O. / Jaehrling, J. / Ettenberg, S.A. / Buckler, A. / Blacklow, S.C. / Aster, J.C. / Fryer, C.J.
History
DepositionAug 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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 / _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 1.3Sep 27, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Neurogenic locus notch homolog protein 3
B: Neurogenic locus notch homolog protein 3
C: 20358 Fab heavy chain
D: 20358 Fab light chain
H: 20358 Fab heavy chain
L: 20358 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,61527
Polymers155,2056
Non-polymers1,41021
Water15,313850
1
A: Neurogenic locus notch homolog protein 3
H: 20358 Fab heavy chain
L: 20358 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,32514
Polymers77,6033
Non-polymers72311
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-32 kcal/mol
Surface area29590 Å2
MethodPISA
2
B: Neurogenic locus notch homolog protein 3
C: 20358 Fab heavy chain
D: 20358 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,29013
Polymers77,6033
Non-polymers68710
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-38 kcal/mol
Surface area29500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.340, 123.860, 150.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Antibody , 2 types, 4 molecules CHDL

#2: Antibody 20358 Fab heavy chain / IgG20358 heavy chain / NVP-LMW985 heavy chain


Mass: 24117.953 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: Antibody 20358 Fab light chain / IgG20358 light chain / NVP-LMW985 light chain


Mass: 23387.939 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

-
Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Neurogenic locus notch homolog protein 3 / Notch 3


Mass: 30096.623 Da / Num. of mol.: 2
Fragment: negative regulatory region (UNP residues 1378-1640)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NOTCH3 / Cell line (production host): HEK / Production host: Homo sapiens (human) / References: UniProt: Q9UM47
#4: 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: 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

-
Non-polymers , 4 types, 869 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 850 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Hepes, pH 7.5, 10% PEG8000, 10% ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 96057 / % possible obs: 99.2 % / Redundancy: 5.1 % / Biso Wilson estimate: 32.06 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 12.56
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.27 / % possible all: 95.9

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
BUSTER2.11.2refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OO4

2oo4


Resolution: 2.1→29.99 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.226 4809 5.01 %Random selection
Rwork0.19 ---
obs-95994 99.2 %-
Displacement parametersBiso mean: 37.37 Å2
Baniso -1Baniso -2Baniso -3
1-3.5181 Å2--
2---10.7451 Å2-
3---7.227 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10002 0 77 850 10929
LS refinement shellResolution: 2.1→2.16 Å
RfactorNum. reflection% reflection
Rfree0.2225 349 5.21 %
Rwork0.1977 6354 -
obs--99.1 %

+
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://pdbjlvh1.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