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- PDB-2ymy: Structure of the murine Nore1-Sarah domain -

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Basic information

Entry
Database: PDB / ID: 2ymy
TitleStructure of the murine Nore1-Sarah domain
ComponentsRAS ASSOCIATION DOMAIN-CONTAINING PROTEIN 5
KeywordsAPOPTOSIS / TUMOR SUPPRESSOR / COILED-COIL / RAS ASSOCIATION DOMAIN FAMILY
Function / homology
Function and homology information


negative regulation of lymphocyte proliferation / lymphocyte proliferation / regulation of protein localization to nucleus / positive regulation of protein ubiquitination / microtubule / apoptotic process / signal transduction / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Ras association domain-containing protein 5 / Ras association domain-containing protein 1-6 / Novel Ras effector 1 C-terminal SARAH (Sav/Rassf/Hpo) domain / SARAH domain / SARAH domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras-associating (RA) domain ...Ras association domain-containing protein 5 / Ras association domain-containing protein 1-6 / Novel Ras effector 1 C-terminal SARAH (Sav/Rassf/Hpo) domain / SARAH domain / SARAH domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Ubiquitin-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Ras association domain-containing protein 5
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.69 Å
AuthorsMakbul, C. / Schwarz, D. / Aruxandei, D.C. / Wolf, E. / Hofmann, E. / Herrmann, C.
CitationJournal: Biochemistry / Year: 2013
Title: Structural and Thermodynamic Characterization of Nore1-Sarah: A Small, Helical Module Important in Signal Transduction Networks.
Authors: Makbul, C. / Constantinescu Aruxandei, D. / Hofmann, E. / Schwarz, D. / Wolf, E. / Herrmann, C.
History
DepositionOct 10, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Other
Revision 2.0May 8, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: RAS ASSOCIATION DOMAIN-CONTAINING PROTEIN 5
B: RAS ASSOCIATION DOMAIN-CONTAINING PROTEIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2685
Polymers10,9302
Non-polymers3373
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-13.7 kcal/mol
Surface area6700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.820, 84.410, 39.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-1409-

CD

21A-2005-

HOH

31A-2031-

HOH

41A-2036-

HOH

51B-2023-

HOH

61B-2041-

HOH

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Components

#1: Protein/peptide RAS ASSOCIATION DOMAIN-CONTAINING PROTEIN 5 / NEW RAS EFFECTOR 1 / REGULATOR FOR CELL ADHESION AND POLARIZATION ENRICHED IN LYMPHOID TISSUES / RAPL / NORE1


Mass: 5465.176 Da / Num. of mol.: 2 / Fragment: SARAH DOMAIN, RESIDUES 370-413
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5EBH1
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.68 Å3/Da / Density % sol: 54.15 % / Description: NONE
Crystal growpH: 4.6
Details: 25-26 % (V/V) PEG 400, 100 MM SODIUM ACETATE (PH 4.6), 45-50 MM CADMIUM CHLORIDE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 1, 2002
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.69→42.21 Å / Num. obs: 13449 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 21.33 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.3
Reflection shellResolution: 1.69→1.73 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.4 / % possible all: 95.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.69→42.205 Å / SU ML: 0.2 / σ(F): 1.35 / Phase error: 26.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2353 663 4.9 %
Rwork0.1943 --
obs0.1963 13436 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0 Å2 / ksol: 0 e/Å3
Displacement parametersBiso mean: 28.8 Å2
Refinement stepCycle: LAST / Resolution: 1.69→42.205 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms698 0 3 88 789
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013740
X-RAY DIFFRACTIONf_angle_d1.406986
X-RAY DIFFRACTIONf_dihedral_angle_d16.114312
X-RAY DIFFRACTIONf_chiral_restr0.072101
X-RAY DIFFRACTIONf_plane_restr0.006132
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.82050.28371250.24262451X-RAY DIFFRACTION97
1.8205-2.00370.23641200.20762531X-RAY DIFFRACTION100
2.0037-2.29370.2411380.17272561X-RAY DIFFRACTION100
2.2937-2.88970.20351400.18912562X-RAY DIFFRACTION100
2.8897-42.21810.24251400.19472668X-RAY DIFFRACTION99

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