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- PDB-4zlp: Crystal Structure of Notch3 Negative Regulatory Region -

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Basic information

Entry
Database: PDB / ID: 4zlp
TitleCrystal Structure of Notch3 Negative Regulatory Region
ComponentsNeurogenic locus notch homolog protein 3
KeywordsTRANSCRIPTION / Notch / Mutation / Disease / Autoinhibiton
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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Neurogenic locus notch homolog protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.479 Å
AuthorsXu, X. / Blacklow, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA092433 to Stephen C Blacklow United States
CitationJournal: Structure / Year: 2015
Title: Insights into Autoregulation of Notch3 from Structural and Functional Studies of Its Negative Regulatory Region.
Authors: Xu, X. / Choi, S.H. / Hu, T. / Tiyanont, K. / Habets, R. / Groot, A.J. / Vooijs, M. / Aster, J.C. / Chopra, R. / Fryer, C. / Blacklow, S.C.
History
DepositionMay 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _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 2.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,79815
Polymers60,1932
Non-polymers1,60513
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-3 kcal/mol
Surface area22740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.482, 64.310, 83.089
Angle α, β, γ (deg.)90.00, 105.23, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-5225-

HOH

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 30096.623 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NOTCH3 / Cell line (production host): HEK293S GnTi- / Production host: Homo sapiens (human) / References: UniProt: Q9UM47

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}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.: 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

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Non-polymers , 4 types, 159 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.11 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 20% isopropanol, 20% PEG4000, and 0.1 M tri-sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 17, 2013
RadiationMonochromator: Cryogenically-cooled single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.479→49.18 Å / Num. obs: 22317 / % possible obs: 99.99 % / Redundancy: 7.5 % / Net I/σ(I): 13.27
Reflection shellResolution: 2.479→2.57 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 2.23 / % possible all: 99.87

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.479→49.176 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2036 1141 5.11 %Random selection
Rwork0.1781 ---
obs0.1795 22314 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.479→49.176 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3450 0 96 148 3694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083679
X-RAY DIFFRACTIONf_angle_d1.0514920
X-RAY DIFFRACTIONf_dihedral_angle_d12.6211313
X-RAY DIFFRACTIONf_chiral_restr0.042536
X-RAY DIFFRACTIONf_plane_restr0.005661
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4792-2.5920.30911470.24882612X-RAY DIFFRACTION100
2.592-2.72870.24751190.21722637X-RAY DIFFRACTION100
2.7287-2.89960.24251180.21562654X-RAY DIFFRACTION100
2.8996-3.12350.2551370.19452646X-RAY DIFFRACTION100
3.1235-3.43770.20631410.18032639X-RAY DIFFRACTION100
3.4377-3.9350.16941580.15912627X-RAY DIFFRACTION100
3.935-4.95690.18631720.14682651X-RAY DIFFRACTION100
4.9569-49.18580.18391490.17222707X-RAY DIFFRACTION100
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)
14.2027-0.5854-0.41985.3201-0.35123.8033-0.1045-0.04590.72490.07480.0795-0.9399-0.42750.48950.01670.2695-0.02050.00980.27750.01120.5835116.057642.2597-39.4432
21.8109-1.94541.98886.2577-1.52163.90330.0325-0.0439-0.2143-0.0810.01310.11660.287-0.0279-0.02140.1821-0.01930.02680.1857-0.00480.2637101.874525.9561-40.054
32.97450.8733-0.95712.9072-0.82571.04090.0357-0.2624-0.1260.2894-0.0331-0.39120.0020.1230.00140.20260.0302-0.05710.1934-0.02890.228116.918313.3926-28.6964
44.08660.0229-0.6762.15330.57424.1007-0.03940.19590.26580.18970.1724-0.6577-0.17290.4997-0.07890.24290.0063-0.04560.22280.03610.4052128.769119.6587-34.5939
52.99280.22970.79163.08470.29462.1050.00630.14730.1766-0.19740.0425-0.40620.05360.0538-0.02770.20720.0302-0.01660.15550.00080.2458114.618821.5659-39.7406
66.0431-0.64-1.02173.89470.8364.2556-0.116-2.01720.53551.70110.04720.2932-0.1472-0.28990.06361.66880.00480.11651.4665-0.05180.699997.30516.837419.066
75.3921-0.0464-1.27353.43720.60535.005-0.6378-1.45750.18941.43830.35740.00480.27650.22870.23211.20860.00130.0361.2010.02470.4469100.4419-0.780115.8872
86.56230.0074-1.45253.76511.59684.7845-0.3246-1.2203-0.34520.98460.1708-0.42060.30580.7860.11451.03410.0118-0.26551.0660.14780.6031114.9472-5.24828.8759
92.9747-0.0001-2.29534.33970.22284.71840.1125-0.56380.04340.97060.0504-0.2520.29140.50890.07620.5015-0.0154-0.03820.40620.02480.2519108.97323.2887-13.1239
103.1544-0.9747-1.63483.02460.03984.6807-0.1294-0.3467-0.51080.6645-0.23770.73580.5115-0.89020.2880.6663-0.1750.11660.6936-0.0440.444293.8903-2.0887-6.0592
112.9566-0.27790.54246.83510.0455.73130.0311-1.044-0.21951.1998-0.1113-0.08880.7423-0.02260.10970.9599-0.05730.10010.76940.10970.4233102.2389-3.39382.328
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1385 through 1425 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1426 through 1468 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1469 through 1539 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1540 through 1587 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1588 through 1637 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1392 through 1407 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1408 through 1425 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1426 through 1462 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1463 through 1498 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1499 through 1587 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1588 through 1633 )

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