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- PDB-4yu8: Crystal structure of Neuroblastoma suppressor of tumorigenicity 1 -

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Basic information

Entry
Database: PDB / ID: 4yu8
TitleCrystal structure of Neuroblastoma suppressor of tumorigenicity 1
ComponentsNeuroblastoma suppressor of tumorigenicity 1
KeywordsANTITUMOR PROTEIN / BMP Binding Protein / NBL1 DAN domain family member 1 BMP-binding / Structural Genomics / Oxford Protein Production Facility / OPPF
Function / homology
Function and homology information


sequestering of BMP from receptor via BMP binding / sequestering of BMP in extracellular matrix / negative regulation of monocyte chemotaxis / determination of dorsal identity / morphogen activity / BMP binding / negative regulation of BMP signaling pathway / positive regulation of neuron differentiation / neuron projection morphogenesis / nervous system development ...sequestering of BMP from receptor via BMP binding / sequestering of BMP in extracellular matrix / negative regulation of monocyte chemotaxis / determination of dorsal identity / morphogen activity / BMP binding / negative regulation of BMP signaling pathway / positive regulation of neuron differentiation / neuron projection morphogenesis / nervous system development / receptor ligand activity / extracellular space / identical protein binding
Similarity search - Function
Neuroblastoma suppressor of tumourigenicity 1 / DAN / DAN domain / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / Cystine-knot cytokine
Similarity search - Domain/homology
Neuroblastoma suppressor of tumorigenicity 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRen, J. / Nettleship, J.E. / Stammers, D.K. / Owens, R.J. / Oxford Protein Production Facility (OPPF)
CitationJournal: To Be Published
Title: Crystal structure of Neuroblastoma suppressor of tumorigenicity 1
Authors: Ren, J. / Nettleship, J.E. / Stammers, D.K. / Owens, R.J.
History
DepositionMar 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
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_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.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 10, 2024Group: 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 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neuroblastoma suppressor of tumorigenicity 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4243
Polymers15,1101
Non-polymers3132
Water90150
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area490 Å2
ΔGint4 kcal/mol
Surface area5210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.069, 37.069, 127.856
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Neuroblastoma suppressor of tumorigenicity 1 / DAN domain family member 1 / Protein N03 / Zinc finger protein DAN


Mass: 15110.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NBL1, DAN, DAND1 / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: P41271
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
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: 1.68 Å3/Da / Density % sol: 26.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG3350 25 %w/v, Magnesium Chloride 0.2M, bis-Tris 0.1M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.278 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 14, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.278 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 10031 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 18.2 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 59
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 2.3 / % possible all: 94.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4x1j

4x1j


Resolution: 1.8→42.62 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 8.111 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25778 479 4.8 %RANDOM
Rwork0.21411 ---
obs0.21605 9496 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.872 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20.2 Å2-0 Å2
2--0.39 Å20 Å2
3----1.27 Å2
Refinement stepCycle: 1 / Resolution: 1.8→42.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms547 0 20 50 617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.019606
X-RAY DIFFRACTIONr_bond_other_d0.0010.02571
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.967826
X-RAY DIFFRACTIONr_angle_other_deg0.76531329
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.81578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24325.83324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.34915106
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.703152
X-RAY DIFFRACTIONr_chiral_restr0.0770.296
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021671
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02125
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.012.559297
X-RAY DIFFRACTIONr_mcbond_other0.9992.55296
X-RAY DIFFRACTIONr_mcangle_it1.7973.809371
X-RAY DIFFRACTIONr_mcangle_other1.7963.819372
X-RAY DIFFRACTIONr_scbond_it1.2412.825309
X-RAY DIFFRACTIONr_scbond_other1.2392.831310
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.084.156453
X-RAY DIFFRACTIONr_long_range_B_refined4.64820.645616
X-RAY DIFFRACTIONr_long_range_B_other4.29920.204597
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.803→1.849 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 36 -
Rwork0.36 657 -
obs--92.15 %
Refinement TLS params.Method: refined / Origin x: 12.7061 Å / Origin y: -8.1137 Å / Origin z: 4.4482 Å
111213212223313233
T0.108 Å2-0.0594 Å20.0015 Å2-0.048 Å2-0.0034 Å2--0.0032 Å2
L1.7637 °20.3718 °2-1.4767 °2-2.0532 °2-0.4646 °2--9.3565 °2
S0.0498 Å °-0.1005 Å °0.02 Å °-0.0517 Å °-0.0126 Å °0.0787 Å °-0.2353 Å °0.0502 Å °-0.0372 Å °

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