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- PDB-5czx: Crystal structure of Notch3 NRR in complex with 20358 Fab -

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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 / 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 / axon guidance / NOTCH3 Activation and Transmission of Signal to the Nucleus / 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 ...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 domain / LNR (Lin-12/Notch) repeat profile. / Notch domain / Domain found in Notch and Lin-12 / EGF-like, conserved site / Human growth factor-like EGF / : / Calcium-binding EGF domain / 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
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 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

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Components

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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)

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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

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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

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Details

Has protein modificationY

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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: 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

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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

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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 %

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