[English] 日本語
Yorodumi
- PDB-5czv: Crystal structure of Notch3 NRR in complex with 20350 Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5czv
TitleCrystal structure of Notch3 NRR in complex with 20350 Fab
Components
  • Fab 20350 heavy chain
  • Fab 20350 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 / artery morphogenesis / NOTCH3 Intracellular Domain Regulates Transcription / Notch-HLH transcription pathway ...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 / artery morphogenesis / NOTCH3 Intracellular Domain Regulates Transcription / Notch-HLH transcription pathway / negative regulation of neuron differentiation / forebrain development / Notch signaling pathway / NOTCH3 Activation and Transmission of Signal to the Nucleus / axon guidance / positive regulation of smooth muscle cell proliferation / 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 / negative regulation of transcription by RNA polymerase II / enzyme binding / 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-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. / 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: 3.19 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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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
H: Fab 20350 heavy chain
L: Fab 20350 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7907
Polymers77,4483
Non-polymers3414
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-29 kcal/mol
Surface area28240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.917, 104.349, 92.849
Angle α, β, γ (deg.)90.000, 113.170, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
Antibody , 2 types, 2 molecules HL

#2: Antibody Fab 20350 heavy chain / IgG20350 heavy chain / NVP-LMW976 heavy chain


Mass: 23794.674 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Antibody Fab 20350 light chain / IgG20350 light chain / NVP-LMW976 light chain


Mass: 23557.186 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

-
Protein / Sugars , 2 types, 2 molecules A

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


Mass: 30096.623 Da / Num. of mol.: 1
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): HEK293-FS / Production host: Homo sapiens (human) / References: UniProt: Q9UM47
#5: 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.: 1
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 , 2 types, 10 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.64 Å3/Da / Density % sol: 53.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 0.1M NaAc, pH 5.6, 17.5% (v/v) PEG3000

-
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 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.19→30 Å / Num. obs: 11614 / % possible obs: 86.4 % / Redundancy: 2.6 % / Biso Wilson estimate: 57.68 Å2 / Rmerge(I) obs: 0.126 / Χ2: 1.043 / Net I/av σ(I): 6.412 / Net I/σ(I): 4.8 / Num. measured all: 29800
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.19-3.262.40.2725390.45979.1
3.26-3.312.50.2435400.52679.8
3.31-3.382.40.2475150.61580.7
3.38-3.452.40.2065320.65679.4
3.45-3.522.50.1845600.63182.7
3.52-3.62.60.1775740.65585.3
3.6-3.692.60.1735650.76885.2
3.69-3.792.60.1935640.65585.2
3.79-3.92.60.1585690.73885.1
3.9-4.032.60.1325980.71988.5
4.03-4.172.60.1255790.7986.4
4.17-4.342.60.1085960.89388
4.34-4.542.40.1125651.00785.7
4.54-4.782.50.1115761.08786.5
4.78-5.072.50.1026030.87389.3
5.07-5.462.60.1156051.52390.6
5.46-6.012.80.1196261.06793.4
6.01-6.872.70.1226351.1892.6
6.87-8.622.50.1036272.31491.3
8.62-302.60.0786462.97993.2

-
Processing

Software
NameVersionClassification
BUSTER-TNTrefinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
BUSTER2.11.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3ETO

3eto


Resolution: 3.19→29.62 Å / Cor.coef. Fo:Fc: 0.8811 / Cor.coef. Fo:Fc free: 0.809 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.539
RfactorNum. reflection% reflectionSelection details
Rfree0.2565 567 4.88 %RANDOM
Rwork0.2036 ---
obs0.2062 11612 85.94 %-
Displacement parametersBiso max: 181.56 Å2 / Biso mean: 68.65 Å2 / Biso min: 9.19 Å2
Baniso -1Baniso -2Baniso -3
1-8.2877 Å20 Å2-2.4135 Å2
2--4.8788 Å20 Å2
3----13.1665 Å2
Refine analyzeLuzzati coordinate error obs: 0.577 Å
Refinement stepCycle: final / Resolution: 3.19→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4915 0 17 7 4939
Biso mean--102.76 16.34 -
Num. residues----642
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1684SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes117HARMONIC2
X-RAY DIFFRACTIONt_gen_planes741HARMONIC5
X-RAY DIFFRACTIONt_it5060HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion650SEMIHARMONIC5
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_contact5599SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5060HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6887HARMONIC21.23
X-RAY DIFFRACTIONt_omega_torsion3.19
X-RAY DIFFRACTIONt_other_torsion21.34
LS refinement shellResolution: 3.19→3.49 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2511 132 5.23 %
Rwork0.2124 2391 -
all0.2145 2523 -
obs--85.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.78330.3910.14791.63880.39421.4174-0.09750.1829-0.3997-0.09580.0516-0.12730.14780.21560.0459-0.0454-0.0046-0.136-0.33640.05890.2297-5.638-17.5861-44.5322
22.70240.907-0.2364.21761.57082.80210.0855-0.73330.12520.52250.0257-0.09820.0737-0.1434-0.1112-0.10050.0991-0.1846-0.17990.0894-0.1126.85279.4536-7.7014
30.52470.4972-0.59281.50781.46051.72160.0445-0.54360.10.35550.3173-0.6029-0.02870.4095-0.3617-0.1310.0375-0.3045-0.1357-0.03930.311419.39216.0591-19.6693
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1391 - 1633
2X-RAY DIFFRACTION2{ H|* }H1 - 216
3X-RAY DIFFRACTION3{ L|* }L2 - 212

+
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