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- PDB-3q13: The Structure of the Ca2+-binding, Glycosylated F-spondin Domain ... -

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Basic information

Entry
Database: PDB / ID: 3q13
TitleThe Structure of the Ca2+-binding, Glycosylated F-spondin Domain of F-spondin, A C2-domain Variant from Extracellular Matrix
ComponentsSpondin-1
KeywordsCELL ADHESION / F-spondin / FS-domain / membrane targeting / axon guidance / C2-domain derivative / Glycosylated / extracellular matrix
Function / homology
Function and homology information


positive regulation of amyloid precursor protein catabolic process / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / positive regulation of protein processing / extracellular matrix structural constituent / LBD domain binding / negative regulation of amyloid-beta formation / extracellular matrix / protein processing / cell adhesion ...positive regulation of amyloid precursor protein catabolic process / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / positive regulation of protein processing / extracellular matrix structural constituent / LBD domain binding / negative regulation of amyloid-beta formation / extracellular matrix / protein processing / cell adhesion / endoplasmic reticulum lumen / extracellular space / metal ion binding
Similarity search - Function
F-spondin domain / Spondin, N-terminal / Spondin, N-terminal domain superfamily / Reeler domain / Spondin_N / Spondin domain profile. / Reeler domain / Reeler domain superfamily / Reelin domain profile. / Spondin-like TSP1 domain ...F-spondin domain / Spondin, N-terminal / Spondin, N-terminal domain superfamily / Reeler domain / Spondin_N / Spondin domain profile. / Reeler domain / Reeler domain superfamily / Reelin domain profile. / Spondin-like TSP1 domain / Spondin-like TSP1 domain / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Spondin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsTan, K. / Lawler, J.
CitationJournal: Bmc Struct.Biol. / Year: 2011
Title: The structure of the Ca2+-binding, glycosylated F-spondin domain of F-spondin - A C2-domain variant in an extracellular matrix protein.
Authors: Tan, K. / Lawler, J.
History
DepositionDec 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_label_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.value / _pdbx_struct_special_symmetry.label_asym_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.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spondin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9037
Polymers28,9291
Non-polymers9746
Water6,197344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Spondin-1
hetero molecules

A: Spondin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,80714
Polymers57,8592
Non-polymers1,94812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Buried area3930 Å2
ΔGint-119 kcal/mol
Surface area24510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.244, 120.244, 86.362
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11A-623-

SO4

21A-1044-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Spondin-1 / F-spondin / Vascular smooth muscle cell growth-promoting factor


Mass: 28929.461 Da / Num. of mol.: 1 / Fragment: UNP residues 191-434
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Homo sapiens, KIAA0762, SPON1, VSGP / Plasmid: pMT/BiP V5-HisA / Cell (production host): Schneider 2 / Production host: Drosophila (fruit flies) / Strain (production host): Drosophila Schneider 2 cell / References: UniProt: Q9HCB6
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 349 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 3.11 Å3/Da / Density % sol: 60.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Lithium sulfate monohydrate, 25% (w/v) PEG 3350, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2007 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.95→104.13 Å / Num. all: 27484 / Num. obs: 27484 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 23.4
Reflection shellResolution: 1.95→2 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.646 / Mean I/σ(I) obs: 3.4 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB:3D34

3d34


Resolution: 1.95→104.13 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.41 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20982 1374 5 %RANDOM
Rwork0.16677 ---
obs0.16885 25973 99.34 %-
all-25965 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.972 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å2-0.17 Å20 Å2
2---0.34 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.95→104.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1853 0 59 344 2256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222032
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.982793
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2955254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22524.67492
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49515330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2131512
X-RAY DIFFRACTIONr_chiral_restr0.1160.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211557
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.8881.51217
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.58121989
X-RAY DIFFRACTIONr_scbond_it2.7533815
X-RAY DIFFRACTIONr_scangle_it4.44.5793
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.946→1.997 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 103 -
Rwork0.207 1846 -
obs--98.29 %
Refinement TLS params.Method: refined / Origin x: -0.9803 Å / Origin y: 46.371 Å / Origin z: 23.2663 Å
111213212223313233
T0.0247 Å20.0019 Å2-0.0014 Å2-0.0161 Å2-0.0044 Å2--0.0131 Å2
L0.3331 °2-0.0959 °20.1578 °2-0.3179 °2-0.2012 °2--0.3235 °2
S0.0003 Å °-0.0008 Å °-0.0311 Å °-0.0675 Å °0.0278 Å °0.0223 Å °0.0561 Å °0.0101 Å °-0.028 Å °

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