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- PDB-1nub: HELIX C DELETION MUTANT OF BM-40 FS-EC DOMAIN PAIR -

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Basic information

Entry
Database: PDB / ID: 1nub
TitleHELIX C DELETION MUTANT OF BM-40 FS-EC DOMAIN PAIR
ComponentsBASEMENT MEMBRANE PROTEIN BM-40
KeywordsEXTRACELLULAR MODULE / GLYCOPROTEIN / ANTI-ADHESIVE PROTEIN / COLLAGEN BINDING / SITE-DIRECTED MUTAGENESIS / GLYCOSYLATED PROTEIN
Function / homology
Function and homology information


semicircular canal morphogenesis / Scavenging by Class H Receptors / platelet alpha granule / platelet alpha granule membrane / regulation of cell morphogenesis / extracellular matrix binding / regulation of synapse organization / negative regulation of endothelial cell proliferation / basement membrane / ECM proteoglycans ...semicircular canal morphogenesis / Scavenging by Class H Receptors / platelet alpha granule / platelet alpha granule membrane / regulation of cell morphogenesis / extracellular matrix binding / regulation of synapse organization / negative regulation of endothelial cell proliferation / basement membrane / ECM proteoglycans / Nuclear signaling by ERBB4 / collagen binding / endocytic vesicle lumen / positive regulation of endothelial cell migration / platelet alpha granule lumen / negative regulation of angiogenesis / nuclear matrix / Platelet degranulation / : / intracellular membrane-bounded organelle / calcium ion binding / cell surface / extracellular space / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
SPARC / Osteonectin-like, conserved site / SPARC/Testican, calcium-binding domain / Osteonectin domain signature 1. / Osteonectin domain signature 2. / Secreted protein acidic and rich in cysteine Ca binding region / Follistatin/Osteonectin EGF domain / Follistatin/Osteonectin-like EGF domain / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like ...SPARC / Osteonectin-like, conserved site / SPARC/Testican, calcium-binding domain / Osteonectin domain signature 1. / Osteonectin domain signature 2. / Secreted protein acidic and rich in cysteine Ca binding region / Follistatin/Osteonectin EGF domain / Follistatin/Osteonectin-like EGF domain / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / EF-hand / Recoverin; domain 1 / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand domain pair / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHohenester, E. / Sasaki, T. / Timpl, R.
Citation
Journal: EMBO J. / Year: 1998
Title: Crystal structure and mapping by site-directed mutagenesis of the collagen-binding epitope of an activated form of BM-40/SPARC/osteonectin.
Authors: Sasaki, T. / Hohenester, E. / Gohring, W. / Timpl, R.
#1: Journal: Embo J. / Year: 1997
Title: Crystal Structure of a Pair of Follistatin-Like and EF-Hand Calcium-Binding Domains in Bm-40
Authors: Hohenester, E. / Maurer, P. / Timpl, R.
#2: Journal: Faseb J. / Year: 1994
Title: The Biology of Sparc, a Protein that Modulates Cell-Matrix Interactions
Authors: Lane, T.F. / Sage, E.H.
History
DepositionDec 5, 1997Processing site: BNL
Revision 1.0Dec 30, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / 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_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / 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.type / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.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.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_conn_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Apr 3, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 13, 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: BASEMENT MEMBRANE PROTEIN BM-40
B: BASEMENT MEMBRANE PROTEIN BM-40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,12810
Polymers53,0392
Non-polymers1,0898
Water00
1
A: BASEMENT MEMBRANE PROTEIN BM-40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0645
Polymers26,5191
Non-polymers5454
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BASEMENT MEMBRANE PROTEIN BM-40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0645
Polymers26,5191
Non-polymers5454
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.860, 88.140, 153.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, -0.0028, -0.0011), (-0.0029, 0.9971, 0.0762), (0.0009, 0.0762, -0.9971)
Vector: 0.2711, 0.1851, -1.7108)

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Components

#1: Protein BASEMENT MEMBRANE PROTEIN BM-40 / OSTEONECTIN / SPARC / SECRETED PROTEIN ACIDIC AND RICH IN CYSTEINE


Mass: 26519.266 Da / Num. of mol.: 2
Fragment: FS-EC DOMAIN PAIR, FS, FOLLISTATIN-LIKE, EC, EXTRACELLULAR CALCIUM-BINDING
Mutation: DEL(1-52, 196-203)
Source method: isolated from a genetically manipulated source
Details: HELIX C (RESIDUES 196-203) DELETION MUTANT / Source: (gene. exp.) Homo sapiens (human) / Cell line: 293-EBNA / Organ: KIDNEY / Cell line (production host): 293-EBNA / Production host: Homo sapiens (human) / References: UniProt: P09486
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
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: 3.5 Å3/Da / Density % sol: 65 %
Description: ROTATION FUNCTION (15-3.5 A): 6.8 SIGMA, HIGHEST HIGHEST NOISE PEAK 2.9 SIGMA. TRANSLATION FUNCTION MOLECULE 1 (6-2.8 A): R-FACTOR 0.511. TRANSLATION FUNCTION MOLECULE 2 (6-2.8 A): R- ...Description: ROTATION FUNCTION (15-3.5 A): 6.8 SIGMA, HIGHEST HIGHEST NOISE PEAK 2.9 SIGMA. TRANSLATION FUNCTION MOLECULE 1 (6-2.8 A): R-FACTOR 0.511. TRANSLATION FUNCTION MOLECULE 2 (6-2.8 A): R-FACTOR 0.514. RIGID-BODY REFINEMENT OF MOLECULES 1 AND 2 (6-2.8 A): R-FACTOR 0.433. 2-FOLD NCS AVERAGING PERFORMED WITH RAVE.
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: HANGING DROP VAPOUR DIFFUSION AT ROOM TEMPERATURE. PROTEIN SOLUTION: 8-10 MG/ML IN 10 MM TRIS PH 7.5, 2 MM CACL2. RESERVOIR SOLUTION: 0.1 M HEPES PH 7.5, 12-14% (W/V) PEG4000, 10% (V/V) 2- ...Details: HANGING DROP VAPOUR DIFFUSION AT ROOM TEMPERATURE. PROTEIN SOLUTION: 8-10 MG/ML IN 10 MM TRIS PH 7.5, 2 MM CACL2. RESERVOIR SOLUTION: 0.1 M HEPES PH 7.5, 12-14% (W/V) PEG4000, 10% (V/V) 2-PROPANOL., vapor diffusion - hanging drop
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: protein solution was mixed with an equal volume of reservoir solution in the drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
210 mMTris-HCl1drop
32 mM1dropCaCl2
412-14 %(w/v)PEG40001reservoir
510 %(v/v)2-propanol1reservoir
6100 mMNa-HEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→15 Å / Num. obs: 17878 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 6.6
Reflection shellResolution: 2.8→2.92 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 1.8 / % possible all: 100
Reflection
*PLUS
Num. measured all: 98015
Reflection shell
*PLUS
% possible obs: 99.5 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4(SCALA)data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BM-40 FS/EC DOMAIN PAIR WITH RESIDUES 168-208 REMOVED

Resolution: 2.8→6 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / Isotropic thermal model: INDIVIDUAL RESTRAINED / Cross valid method: FREE R-FACTOR / σ(F): 0
Details: ATOMS NOT DEFINED BY THE ELECTRON DENSITY WERE REFINED WITH ZERO OCCUPANCY
RfactorNum. reflection% reflectionSelection details
Rfree0.306 1671 10.3 %RANDOM
Rwork0.255 ---
obs0.255 16014 99.7 %-
Displacement parametersBiso mean: 26 Å2
Refinement stepCycle: LAST / Resolution: 2.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3670 0 62 0 3732
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSRms dev Biso : 0 Å2 / Rms dev position: 0 Å
LS refinement shellResolution: 2.8→2.96 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.381 263 9.9 %
Rwork0.357 2374 -
obs--99.3 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.357

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