[English] 日本語
Yorodumi
- PDB-6xsw: Structure of the Notch3 NRR in complex with an antibody Fab Fragment -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xsw
TitleStructure of the Notch3 NRR in complex with an antibody Fab Fragment
Components
  • Anti-N3 Fab Heavy Chain
  • Anti-N3 Fab Light Chain
  • Neurogenic locus notch homolog protein 3
KeywordsSIGNALING PROTEIN/Immune System / Notch3 / Antibody / SIGNALING PROTEIN / SIGNALING PROTEIN-Immune System complex
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
Neurogenic locus Notch 3 / Notch, C-terminal / Domain of unknown function / Notch / Notch, NOD domain / Notch, NODP domain / NOTCH protein / NOTCH protein / NOD / NODP ...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) / 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
Neurogenic locus notch homolog protein 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsBard, J.
CitationJournal: Cell Rep Med / Year: 2021
Title: NOTCH3-targeted antibody drug conjugates regress tumors by inducing apoptosis in receptor cells and through transendocytosis into ligand cells.
Authors: Geles, K.G. / Gao, Y. / Giannakou, A. / Sridharan, L. / Yamin, T.T. / Zhang, J. / Karim, R. / Bard, J. / Piche-Nicholas, N. / Charati, M. / Maderna, A. / Lucas, J. / Golas, J. / Guffroy, M. ...Authors: Geles, K.G. / Gao, Y. / Giannakou, A. / Sridharan, L. / Yamin, T.T. / Zhang, J. / Karim, R. / Bard, J. / Piche-Nicholas, N. / Charati, M. / Maderna, A. / Lucas, J. / Golas, J. / Guffroy, M. / Pirie-Shepherd, S. / Roy, M. / Qian, J. / Franks, T. / Zhong, W. / O'Donnell, C.J. / Tchistiakova, L. / Gerber, H.P. / Sapra, P.
History
DepositionJul 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Anti-N3 Fab Heavy Chain
B: Anti-N3 Fab Light Chain
C: Neurogenic locus notch homolog protein 3
D: Anti-N3 Fab Heavy Chain
E: Anti-N3 Fab Light Chain
F: Neurogenic locus notch homolog protein 3
G: Anti-N3 Fab Heavy Chain
H: Anti-N3 Fab Heavy Chain
I: Anti-N3 Fab Light Chain
J: Neurogenic locus notch homolog protein 3
L: Anti-N3 Fab Light Chain
X: Neurogenic locus notch homolog protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)318,97928
Polymers317,59112
Non-polymers1,38816
Water18010
1
A: Anti-N3 Fab Heavy Chain
B: Anti-N3 Fab Light Chain
C: Neurogenic locus notch homolog protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7397
Polymers79,3983
Non-polymers3414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Anti-N3 Fab Heavy Chain
E: Anti-N3 Fab Light Chain
F: Neurogenic locus notch homolog protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7397
Polymers79,3983
Non-polymers3414
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Anti-N3 Fab Heavy Chain
I: Anti-N3 Fab Light Chain
J: Neurogenic locus notch homolog protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,5186
Polymers79,3983
Non-polymers1203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
H: Anti-N3 Fab Heavy Chain
L: Anti-N3 Fab Light Chain
X: Neurogenic locus notch homolog protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9828
Polymers79,3983
Non-polymers5855
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.652, 158.951, 159.687
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein , 1 types, 4 molecules CFJX

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


Mass: 31174.955 Da / Num. of mol.: 4
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

-
Antibody , 2 types, 8 molecules ADGHBEIL

#1: Antibody
Anti-N3 Fab Heavy Chain


Mass: 24713.717 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: rat-human chimeric antibody / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line (production host): HEK / Production host: Homo sapiens (human)
#2: Antibody
Anti-N3 Fab Light Chain


Mass: 23509.107 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: rat human chimeric antibody / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line (production host): HEK / Production host: Homo sapiens (human)

-
Sugars , 2 types, 3 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1 / Source method: isolated from a natural source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: 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 natural 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, 23 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 100 mM sodium Citrate pH 5.5, 12 % PEG 6000

-
Data collection

DiffractionMean temperature: 170 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.98→159.69 Å / Num. obs: 70289 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 75.47 Å2 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.079 / Net I/σ(I): 10
Reflection shellResolution: 2.98→3.14 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.099 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 10115 / Rpim(I) all: 0.456 / % possible all: 100

-
Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1xgp

1xgp


Resolution: 2.98→112.66 Å / Cor.coef. Fo:Fc: 0.834 / Cor.coef. Fo:Fc free: 0.829 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.385
RfactorNum. reflection% reflectionSelection details
Rfree0.256 3541 5.04 %RANDOM
Rwork0.233 ---
obs0.234 70204 99.9 %-
Displacement parametersBiso max: 150.49 Å2 / Biso mean: 57.74 Å2 / Biso min: 15.39 Å2
Baniso -1Baniso -2Baniso -3
1--19.2602 Å20 Å20 Å2
2--15.9061 Å20 Å2
3---3.354 Å2
Refine analyzeLuzzati coordinate error obs: 0.49 Å
Refinement stepCycle: final / Resolution: 2.98→112.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18838 0 69 10 18917
Biso mean--61.97 35.53 -
Num. residues----2508
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d6243SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3318HARMONIC5
X-RAY DIFFRACTIONt_it19392HARMONIC20
X-RAY DIFFRACTIONt_nbd10SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2524SEMIHARMONIC5
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_contact20382SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d19392HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg26458HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion2.39
X-RAY DIFFRACTIONt_other_torsion19.74
LS refinement shellResolution: 2.98→3.05 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3293 249 4.86 %
Rwork0.2756 4871 -
all0.2781 5120 -
obs--99.75 %

+
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