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- PDB-2erf: Crystal Structure of the Thrombospondin-1 N-terminal Domain at 1.... -

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Basic information

Entry
Database: PDB / ID: 2erf
TitleCrystal Structure of the Thrombospondin-1 N-terminal Domain at 1.45A Resolution
ComponentsThrombospondin-1Thrombospondin 1
KeywordsSUGAR BINDING PROTEIN / Thrombospondin-1 / TSP-1 / N-terminal TSPN / HBD
Function / homology
Function and homology information


negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / collagen V binding / negative regulation of dendritic cell antigen processing and presentation / negative regulation of nitric oxide mediated signal transduction / chronic inflammatory response / negative regulation of sprouting angiogenesis / negative regulation of endothelial cell chemotaxis / Defective B3GALTL causes PpS / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / O-glycosylation of TSR domain-containing proteins ...negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / collagen V binding / negative regulation of dendritic cell antigen processing and presentation / negative regulation of nitric oxide mediated signal transduction / chronic inflammatory response / negative regulation of sprouting angiogenesis / negative regulation of endothelial cell chemotaxis / Defective B3GALTL causes PpS / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / O-glycosylation of TSR domain-containing proteins / positive regulation of transforming growth factor beta1 production / negative regulation of fibroblast growth factor receptor signaling pathway / negative regulation of long-chain fatty acid import across plasma membrane / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / engulfment of apoptotic cell / low-density lipoprotein particle binding / negative regulation of focal adhesion assembly / fibrinogen complex / peptide cross-linking / positive regulation of chemotaxis / fibrinogen binding / Signaling by PDGF / platelet alpha granule / negative regulation of interleukin-12 production / negative regulation of cell migration involved in sprouting angiogenesis / negative regulation of plasminogen activation / positive regulation of macrophage activation / transforming growth factor beta binding / positive regulation of endothelial cell apoptotic process / negative regulation of endothelial cell migration / positive regulation of fibroblast migration / sprouting angiogenesis / proteoglycan binding / extracellular matrix structural constituent / Syndecan interactions / endopeptidase inhibitor activity / negative regulation of cell-matrix adhesion / phosphatidylserine binding / positive regulation of macrophage chemotaxis / negative regulation of cGMP-mediated signaling / negative regulation of endothelial cell proliferation / response to testosterone / fibroblast growth factor binding / behavioral response to pain / positive regulation of transforming growth factor beta receptor signaling pathway / negative regulation of blood vessel endothelial cell migration / response to magnesium ion / fibronectin binding / response to unfolded protein / positive regulation of blood vessel endothelial cell migration / laminin binding / Integrin cell surface interactions / positive regulation of blood coagulation / negative regulation of fibrinolysis / response to glucose / response to mechanical stimulus / positive regulation of phosphorylation / extracellular matrix / response to endoplasmic reticulum stress / negative regulation of angiogenesis / positive regulation of endothelial cell migration / positive regulation of translation / platelet alpha granule lumen / response to progesterone / sarcoplasmic reticulum / secretory granule / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of smooth muscle cell proliferation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / positive regulation of MAP kinase activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / cellular response to growth factor stimulus / response to calcium ion / positive regulation of angiogenesis / positive regulation of reactive oxygen species metabolic process / cell migration / integrin binding / positive regulation of tumor necrosis factor production / Platelet degranulation / cellular response to heat / heparin binding / cellular response to tumor necrosis factor / collagen-containing extracellular matrix / protease binding / response to hypoxia / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / positive regulation of cell migration / immune response / response to xenobiotic stimulus / inflammatory response / endoplasmic reticulum lumen / negative regulation of cell population proliferation / external side of plasma membrane / apoptotic process / calcium ion binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / cell surface / endoplasmic reticulum
Similarity search - Function
Thrombospondin, C-terminal / Thrombospondin, type 3 repeat / Thrombospondin C-terminal region / Thrombospondin type-3 (TSP3) repeat profile. / Thrombospondin C-terminal domain profile. / Thrombospondin, type 3-like repeat / Thrombospondin type 3 repeat / TSP type-3 repeat / : / Thrombospondin N-terminal -like domains. ...Thrombospondin, C-terminal / Thrombospondin, type 3 repeat / Thrombospondin C-terminal region / Thrombospondin type-3 (TSP3) repeat profile. / Thrombospondin C-terminal domain profile. / Thrombospondin, type 3-like repeat / Thrombospondin type 3 repeat / TSP type-3 repeat / : / Thrombospondin N-terminal -like domains. / EGF domain / EGF domain / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC 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 / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / Jelly Rolls - #200 / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsTan, K. / Wang, J. / Lawler, J.
CitationJournal: Structure / Year: 2006
Title: The structures of the thrombospondin-1 N-terminal domain and its complex with a synthetic pentameric heparin.
Authors: Tan, K. / Duquette, M. / Liu, J.H. / Zhang, R. / Joachimiak, A. / Wang, J.H. / Lawler, J.
History
DepositionOct 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE THE SEQUENCE OF THE WHOLE CONSTRUCT IS LISTED HERE: ...SEQUENCE THE SEQUENCE OF THE WHOLE CONSTRUCT IS LISTED HERE: RSPWNRIPESGGDNSVFDIFELTGAARKGSGRRLVKGPDPSSPAFRIEDA NLIPPVPDDKFQDLVDAVRTEKGFLLLASLRQMKKTRGTLLALERKDHSG QVFSVVSNGKAGTLDLSLTVQGKQHVVSVEEALLATGQWKSITLFVQEDR AQLYIDCEKMENAELDVPIQSVFTRDLASIARLRIAKGGVNDNFQGVLQN VRFVFGTTPEDILRNKGCSSSTSVLLTLDNNVVNGSSPAIRTNTGHHHHHH THE PURIFIED PROTEIN WAS TREATED WITH CHYMOTRYPSIN AND RE-PURIFIED BEFORE CRYSTALLIZATION. THE EXACT N-TERMINAL OR C-TERMINAL SEQUENCES ARE NOT KNOWN. THE SEQRES REPRESENTS THE RESIDUES IN THE COORDINATES.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thrombospondin-1


Theoretical massNumber of molelcules
Total (without water)22,9011
Polymers22,9011
Non-polymers00
Water3,909217
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.310, 40.489, 60.086
Angle α, β, γ (deg.)90.00, 106.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Thrombospondin-1 / Thrombospondin 1


Mass: 22901.035 Da / Num. of mol.: 1 / Fragment: N-terminal Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THBS1, TSP, TSP1 / Cell line (production host): S2 Cell / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P07996
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.2 Å3/Da / Density % sol: 42.7 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 30% PEG1500 and 0.1M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.00931 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 7, 2005
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00931 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. all: 34155 / Num. obs: 34155 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 29.2 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 39.7
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2422 / % possible all: 68.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Z78

1z78


Resolution: 1.45→22.86 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.702 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21672 2575 7.7 %RANDOM
Rwork0.18301 ---
all0.1863 30931 --
obs0.18559 30931 94.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.962 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.45→22.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1609 0 0 217 1826
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221634
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.9742206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1655208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.76224.26775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.20815293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1381514
X-RAY DIFFRACTIONr_chiral_restr0.0960.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021229
X-RAY DIFFRACTIONr_nbd_refined0.2150.2710
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21135
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2187
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.227
X-RAY DIFFRACTIONr_mcbond_it1.4731.51059
X-RAY DIFFRACTIONr_mcangle_it2.2721665
X-RAY DIFFRACTIONr_scbond_it5.4343617
X-RAY DIFFRACTIONr_scangle_it5.1864.5541
X-RAY DIFFRACTIONr_rigid_bond_restr5.60731676
X-RAY DIFFRACTIONr_sphericity_free4.3953217
X-RAY DIFFRACTIONr_sphericity_bonded3.84131610
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 132 -
Rwork0.254 1571 -
obs--66.03 %

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