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- PDB-5fma: human Notch 1, EGF 4-7 -

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Basic information

Entry
Database: PDB / ID: 5fma
Titlehuman Notch 1, EGF 4-7
ComponentsNEUROGENIC LOCUS NOTCH HOMOLOG PROTEIN 1
KeywordsTRANSCRIPTION / TRANSMEMBRANE / DEVELOPMENTAL / PROTEIN / NOTCH SIGNALING PATHWAY / DIFFERENTIATION / PHOSPHORYLATION / EGF- LIKE DOMAIN / REGULATION / RECEPTOR / ACTIVATOR / ANK REPEAT / SIGNALLING / GLYCOPROTEIN / EXTRACELLULAR / EGF / NOTCH / JAGGED / MEMBRANE
Function / homology
Function and homology information


Defective LFNG causes SCDO3 / coronary sinus valve morphogenesis / cardiac right atrium morphogenesis / cardiac right ventricle formation / growth involved in heart morphogenesis / Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation / cell differentiation in spinal cord / retinal cone cell differentiation / venous endothelial cell differentiation / arterial endothelial cell differentiation ...Defective LFNG causes SCDO3 / coronary sinus valve morphogenesis / cardiac right atrium morphogenesis / cardiac right ventricle formation / growth involved in heart morphogenesis / Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation / cell differentiation in spinal cord / retinal cone cell differentiation / venous endothelial cell differentiation / arterial endothelial cell differentiation / cardiac chamber formation / epithelial cell fate commitment / negative regulation of pro-B cell differentiation / Pre-NOTCH Processing in the Endoplasmic Reticulum / negative regulation of inner ear auditory receptor cell differentiation / mitral valve formation / cell migration involved in endocardial cushion formation / glomerular mesangial cell development / negative regulation of photoreceptor cell differentiation / negative regulation of cell proliferation involved in heart valve morphogenesis / regulation of somitogenesis / inhibition of neuroepithelial cell differentiation / endocardium morphogenesis / foregut morphogenesis / regulation of cell adhesion involved in heart morphogenesis / distal tubule development / MAML1-RBP-Jkappa- ICN1 complex / regulation of epithelial cell proliferation involved in prostate gland development / auditory receptor cell fate commitment / positive regulation of aorta morphogenesis / negative regulation of endothelial cell chemotaxis / atrioventricular node development / neuroendocrine cell differentiation / collecting duct development / negative regulation of extracellular matrix constituent secretion / positive regulation of transcription of Notch receptor target / cellular response to tumor cell / positive regulation of apoptotic process involved in morphogenesis / compartment pattern specification / vasculogenesis involved in coronary vascular morphogenesis / T-helper 17 type immune response / regulation of extracellular matrix assembly / endocardial cell differentiation / epithelial to mesenchymal transition involved in endocardial cushion formation / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / cardiac ventricle morphogenesis / positive regulation of smooth muscle cell differentiation / mesenchymal cell development / cardiac left ventricle morphogenesis / epidermal cell fate specification / coronary vein morphogenesis / negative regulation of collagen biosynthetic process / cardiac vascular smooth muscle cell development / negative regulation of myotube differentiation / somatic stem cell division / left/right axis specification / negative regulation of cardiac muscle hypertrophy / negative regulation of cell adhesion molecule production / interleukin-17-mediated signaling pathway / positive regulation of endothelial cell differentiation / apoptotic process involved in embryonic digit morphogenesis / endocardium development / positive regulation of cardiac epithelial to mesenchymal transition / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / Pre-NOTCH Processing in Golgi / cardiac epithelial to mesenchymal transition / cellular response to follicle-stimulating hormone stimulus / pericardium morphogenesis / cardiac atrium morphogenesis / cardiac muscle cell myoblast differentiation / negative regulation of catalytic activity / negative regulation of calcium ion-dependent exocytosis / neuronal stem cell population maintenance / tissue regeneration / regulation of stem cell proliferation / negative regulation of oligodendrocyte differentiation / positive regulation of astrocyte differentiation / calcium-ion regulated exocytosis / pulmonary valve morphogenesis / negative regulation of biomineral tissue development / heart trabecula morphogenesis / endoderm development / coronary artery morphogenesis / negative regulation of cell-cell adhesion mediated by cadherin / luteolysis / prostate gland epithelium morphogenesis / cardiac muscle tissue morphogenesis / ventricular trabecula myocardium morphogenesis / negative regulation of myoblast differentiation / tube formation / negative regulation of cell migration involved in sprouting angiogenesis / transcription regulator activator activity / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / negative regulation of stem cell differentiation / positive regulation of keratinocyte differentiation / positive regulation of BMP signaling pathway / astrocyte differentiation / negative regulation of ossification / inflammatory response to antigenic stimulus / positive regulation of Ras protein signal transduction
Similarity search - Function
Neurogenic locus notch homolog protein 1 / : / Notch, C-terminal / Domain of unknown function / Notch / Notch, NOD domain / Notch, NODP domain / NOTCH protein / NOTCH protein / NOD ...Neurogenic locus notch homolog protein 1 / : / 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 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsWeisshuhn, P.C. / Sheppard, D. / Taylor, P. / Whiteman, P. / Lea, S.M. / Handford, P.A. / Redfield, C.
CitationJournal: Structure / Year: 2016
Title: Non-Linear and Flexible Regions of the Human Notch1 Extracellular Domain Revealed by High-Resolution Structural Studies.
Authors: Weisshuhn, P.C. / Sheppard, D. / Taylor, P. / Whiteman, P. / Lea, S.M. / Handford, P.A. / Redfield, C.
History
DepositionNov 2, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Feb 7, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 1
B: NEUROGENIC LOCUS NOTCH HOMOLOG PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,16210
Polymers32,8282
Non-polymers3338
Water32418
1
A: NEUROGENIC LOCUS NOTCH HOMOLOG PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5344
Polymers16,4141
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NEUROGENIC LOCUS NOTCH HOMOLOG PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6276
Polymers16,4141
Non-polymers2135
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.940, 86.830, 53.450
Angle α, β, γ (deg.)90.00, 107.58, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.118, 0.127, 0.0985), (0.13, -0.981, 0.142), (0.985, 0.144, 0.099)
Vector: -67.541, 61.993, 15.557)

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Components

#1: Protein NEUROGENIC LOCUS NOTCH HOMOLOG PROTEIN 1 / NOTCH 1 / HN1 / TRANSLOCATION-ASSOCIATED NOTCH PROTEIN TAN-1 / HUMAN NOTCH I


Mass: 16414.135 Da / Num. of mol.: 2 / Fragment: EGF DOMAINS 4-7, RESIDUES 142-294
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P46531
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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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: 2.76 Å3/Da / Density % sol: 55.41 % / Description: NONE
Crystal growpH: 6.5 / Details: pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.75
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Feb 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.75 Å / Relative weight: 1
ReflectionResolution: 2.46→33.9 Å / Num. obs: 12129 / % possible obs: 94.1 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 74.22 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.9
Reflection shellResolution: 2.46→2.53 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.3 / % possible all: 93.8

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VJ3

2vj3


Resolution: 2.46→43.42 Å / Cor.coef. Fo:Fc: 0.9011 / Cor.coef. Fo:Fc free: 0.8983 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.53 / SU Rfree Blow DPI: 0.278
RfactorNum. reflection% reflectionSelection details
Rfree0.2634 578 4.77 %RANDOM
Rwork0.2592 ---
obs0.2594 12109 93.14 %-
Displacement parametersBiso mean: 68.95 Å2
Baniso -1Baniso -2Baniso -3
1-11.2342 Å20 Å21.1109 Å2
2---0.9695 Å20 Å2
3----10.2647 Å2
Refine analyzeLuzzati coordinate error obs: 0.81 Å
Refinement stepCycle: LAST / Resolution: 2.46→43.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2219 0 11 18 2248
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0354243HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.217625HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d825SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes69HARMONIC2
X-RAY DIFFRACTIONt_gen_planes697HARMONIC5
X-RAY DIFFRACTIONt_it4243HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.1
X-RAY DIFFRACTIONt_other_torsion17.66
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion292SEMIHARMONIC5
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_contact3931SEMIHARMONIC4
LS refinement shellResolution: 2.46→2.69 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2751 144 5.08 %
Rwork0.3019 2688 -
all0.3005 2832 -
obs--93.14 %
Refinement TLS params.

L22: 0 °2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°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)
11.2727-0.0414-0.99920.21871.36970.2183-0.10320.1309-0.034-0.03810.1525-0.20460.2035-0.1802-0.1073-0.0207-0.025-0.2232-0.0479-0.066931.10449.009797.1812
20.7250.6133-0.5965-0.4641.0646-0.079-0.0366-0.2139-0.194-0.10370.08520.25130.00580.1827-0.07980.0648-0.0556-0.2296-0.0139-0.063131.868831.339463.1594

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