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- PDB-1tdq: Structural basis for the interactions between tenascins and the C... -

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Basic information

Entry
Database: PDB / ID: 1tdq
TitleStructural basis for the interactions between tenascins and the C-type lectin domains from lecticans: evidence for a cross-linking role for tenascins
Components
  • Aggrecan core protein
  • Tenascin-R
Keywordsextracellular matrix / lecticans / tenascins / protein-protein interactions / C-type lectin domain
Function / homology
Function and homology information


Keratan sulfate biosynthesis / Keratan sulfate degradation / negative regulation of axon extension involved in regeneration / : / perineuronal net / ECM proteoglycans / perisynaptic extracellular matrix / Degradation of the extracellular matrix / positive regulation of transmission of nerve impulse / chondrocyte development ...Keratan sulfate biosynthesis / Keratan sulfate degradation / negative regulation of axon extension involved in regeneration / : / perineuronal net / ECM proteoglycans / perisynaptic extracellular matrix / Degradation of the extracellular matrix / positive regulation of transmission of nerve impulse / chondrocyte development / proteoglycan biosynthetic process / chondroblast differentiation / telencephalon cell migration / hyaluronic acid binding / response to gravity / response to xenobiotic stimulus => GO:0009410 / neuron cell-cell adhesion / negative regulation of axon extension / negative regulation of cell adhesion / response to acidic pH / collagen fibril organization / negative regulation of synaptic transmission / cartilage condensation / spinal cord development / negative regulation of cell-cell adhesion / locomotory exploration behavior / associative learning / neuromuscular process controlling balance / basement membrane / GABA-ergic synapse / response to glucose / response to mechanical stimulus / hippocampal mossy fiber to CA3 synapse / positive regulation of synaptic transmission, glutamatergic / negative regulation of cell migration / ossification / extracellular matrix organization / extracellular matrix / skeletal system development / central nervous system development / long-term synaptic potentiation / synapse organization / Schaffer collateral - CA1 synapse / response to radiation / modulation of chemical synaptic transmission / response to organic cyclic compound / cellular response to growth factor stimulus / integrin binding / negative regulation of neuron projection development / nervous system development / heart development / carbohydrate binding / collagen-containing extracellular matrix / cell adhesion / neuron projection / membrane raft / signaling receptor binding / neuronal cell body / glutamatergic synapse / calcium ion binding / cell surface / extracellular space
Similarity search - Function
Tenascin-R / Aggrecan/versican, C-type lectin-like domain / Tenascin, EGF-like domain / Tenascin EGF domain / Link domain / Extracellular link domain / Link domain signature. / Link domain profile. / Link (Hyaluronan-binding) / Fibrinogen-related domains (FReDs) ...Tenascin-R / Aggrecan/versican, C-type lectin-like domain / Tenascin, EGF-like domain / Tenascin EGF domain / Link domain / Extracellular link domain / Link domain signature. / Link domain profile. / Link (Hyaluronan-binding) / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Epidermal growth factor-like domain. / EGF-like domain signature 2. / Fibronectin type III domain / EGF-like domain signature 1. / EGF-like domain / Fibronectin type 3 domain / Immunoglobulin V-Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulin / Immunoglobulins and major histocompatibility complex proteins signature. / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Aggrecan core protein / Tenascin-R
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.6 Å
AuthorsLundell, A. / Olin, A.I. / Moergelin, M. / al-Karadaghi, S. / Aspberg, A. / Logan, D.T.
CitationJournal: Structure / Year: 2004
Title: Structural basis for interactions between tenascins and lectican C-type lectin domains: evidence for a crosslinking role for tenascins
Authors: Lundell, A. / Olin, A.I. / Moergelin, M. / al-Karadaghi, S. / Aspberg, A. / Logan, D.T.
History
DepositionMay 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Mar 31, 2021Group: Database references / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_struct_conn_angle ...entity_src_gen / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _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_auth_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 / _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.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 / _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: Tenascin-R
B: Aggrecan core protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1265
Polymers46,0062
Non-polymers1203
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.52, 86.42, 57.60
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological complex consists of full-lenth aggrecan and tenascin-R, represented here by FnIII domains 3-5 from tenascin (chain A) and the C-type lectin domain of aggrecan (chain B)

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Components

#1: Protein Tenascin-R


Mass: 30326.650 Da / Num. of mol.: 1 / Fragment: fibronectin type III repeats 3-5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / Strain (production host): TG-1 / References: UniProt: Q05546
#2: Protein Aggrecan core protein / Cartilage-specific proteoglycan core protein / CSPCP


Mass: 15679.100 Da / Num. of mol.: 1 / Fragment: C-type lectin domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: AGC1, AGC / Plasmid: pCEP4 / Cell line (production host): embryonal kidney 293-EBNA / Production host: Homo sapiens (human) / References: UniProt: P07897
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.2 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 8-12% PEG 8000, 150mM calcium acetate, 2-4% PEG MME 750, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.097 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 1, 2003 / Details: asymmetrically cut Si(111)
RadiationMonochromator: asymmetrically cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.097 Å / Relative weight: 1
ReflectionResolution: 2.57→39 Å / Num. all: 18221 / Num. obs: 18210 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 66.6 Å2 / Rsym value: 0.072 / Net I/σ(I): 7.2
Reflection shellResolution: 2.57→2.71 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 2421 / Rsym value: 0.198 / % possible all: 91.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.6→39 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.405 / SU ML: 0.186 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.488 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23441 909 5.1 %RANDOM
Rwork0.20862 ---
all0.21 18221 --
obs0.20995 16812 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.979 Å2
Baniso -1Baniso -2Baniso -3
1-1.73 Å20 Å20 Å2
2---2.41 Å20 Å2
3---0.68 Å2
Refinement stepCycle: LAST / Resolution: 2.6→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3140 0 3 38 3181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213217
X-RAY DIFFRACTIONr_bond_other_d0.0020.022794
X-RAY DIFFRACTIONr_angle_refined_deg1.2961.9344381
X-RAY DIFFRACTIONr_angle_other_deg0.81336522
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.415395
X-RAY DIFFRACTIONr_chiral_restr0.0840.2479
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023612
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02654
X-RAY DIFFRACTIONr_nbd_refined0.2030.2568
X-RAY DIFFRACTIONr_nbd_other0.220.23106
X-RAY DIFFRACTIONr_nbtor_other0.0850.22058
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.257
X-RAY DIFFRACTIONr_metal_ion_refined0.1580.28
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2380.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2330.27
X-RAY DIFFRACTIONr_mcbond_it1.85821980
X-RAY DIFFRACTIONr_mcangle_it3.00133222
X-RAY DIFFRACTIONr_scbond_it2.17921237
X-RAY DIFFRACTIONr_scangle_it3.44831159
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.38 70
Rwork0.307 1183
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.3924-0.5306-0.860311.23491.71027.7243-0.3263-0.10290.1680.54410.4591-1.60410.30470.6204-0.13270.18230.0629-0.12120.0218-0.04530.200735.8311-14.571667.7353
22.6176-1.5728-0.28085.6522.49337.91850.35820.3614-0.1449-0.867-0.23230.37960.1859-0.5338-0.12590.2592-0.0362-0.02870.296-0.06510.197311.4146-3.051594.8351
37.9842-6.4732-6.095913.86798.236814.3207-0.1059-0.12880.15990.367-1.30831.136-0.5769-2.80421.41430.14910.16920.04781.0612-0.42530.4596-1.376416.7298123.6301
44.1695-0.28871.73234.7064-1.04985.9253-0.18840.01480.2760.3045-0.041-0.6304-0.39030.44910.22930.2712-0.0388-0.00990.2804-0.0110.422529.94555.2956111.0745
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 9312 - 104
2X-RAY DIFFRACTION2AA94 - 185105 - 196
3X-RAY DIFFRACTION3AA186 - 271197 - 282
4X-RAY DIFFRACTION4BB1 - 1265 - 130
5X-RAY DIFFRACTION4BC - E127 - 1291

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