[English] 日本語
Yorodumi
- PDB-1tn3: THE C-TYPE LECTIN CARBOHYDRATE RECOGNITION DOMAIN OF HUMAN TETRANECTIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tn3
TitleTHE C-TYPE LECTIN CARBOHYDRATE RECOGNITION DOMAIN OF HUMAN TETRANECTIN
ComponentsTETRANECTIN
KeywordsLECTIN / TETRANECTIN / PLASMINOGEN BINDING / KRINGLE 4 / C-TYPE LECTIN / CARBOHYDRATE RECOGNITION DOMAIN
Function / homology
Function and homology information


kringle domain binding / platelet dense granule lumen / granular component / positive regulation of plasminogen activation / : / bone mineralization / cellular response to transforming growth factor beta stimulus / ossification / Platelet degranulation / heparin binding ...kringle domain binding / platelet dense granule lumen / granular component / positive regulation of plasminogen activation / : / bone mineralization / cellular response to transforming growth factor beta stimulus / ossification / Platelet degranulation / heparin binding / carbohydrate binding / collagen-containing extracellular matrix / calcium ion binding / extracellular space / extracellular exosome / extracellular region / cytoplasm
Similarity search - Function
C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / 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 ...C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
ETHANOL / Tetranectin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKastrup, J.S. / Nielsen, B.B. / Rasmussen, H. / Holtet, T.L. / Graversen, J.H. / Etzerodt, M. / Thoegersen, H.C. / Larsen, I.K.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Structure of the C-type lectin carbohydrate recognition domain of human tetranectin.
Authors: Kastrup, J.S. / Nielsen, B.B. / Rasmussen, H. / Holtet, T.L. / Graversen, J.H. / Etzerodt, M. / Thogersen, H.C. / Larsen, I.K.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Human Plasminogen Binding Protein Tetranectin: Crystallization and Preliminary X-Ray Analysis of the C-Type Lectin Crd and the Full-Length Protein
Authors: Kastrup, J.S. / Rasmussen, H. / Nielsen, B.B. / Larsen, I.K. / Holtet, T.L. / Graversen, J.H. / Etzerodt, M. / Thogersen, H.C.
#2: Journal: FEBS Lett. / Year: 1997
Title: Crystal Structure of Tetranectin, a Trimeric Plasminogen-Binding Protein with an Alpha-Helical Coiled Coil
Authors: Nielsen, B.B. / Kastrup, J.S. / Rasmussen, H. / Holtet, T.L. / Graversen, J.H. / Etzerodt, M. / Thogersen, H.C. / Larsen, I.K.
#3: Journal: Protein Sci. / Year: 1997
Title: Tetranectin, a Trimeric Plasminogen-Binding C-Type Lectin
Authors: Holtet, T.L. / Graversen, J.H. / Clemmensen, I. / Thogersen, H.C. / Etzerodt, M.
#4: Journal: FEBS Lett. / Year: 1992
Title: The Gene Structure of Tetranectin, a Plasminogen Binding Protein
Authors: Berglund, L. / Petersen, T.E.
History
DepositionNov 6, 1997Processing site: BNL
Revision 1.0May 6, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TETRANECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3595
Polymers15,1371
Non-polymers2224
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.250, 64.250, 75.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-194-

HOH

21A-216-

HOH

DetailsTHE CARBOHYDRATE RECOGNITION DOMAIN OF TETRANECTIN FORMS A DIMER IN CRYSTALS, WHEREAS FULL-LENGTH TETRANECTIN IS A HOMOTRIMER IN CRYSTALS AS WELL AS IN SOLUTION. TWO DIFFERENT SIDE CHAIN CONFORMATIONS HAVE BEEN IDENTIFIED FOR THR 48, VAL 49, AND MET 58. IN ADDITION, THE AMIDE MOIETIES LINKING THR 138 AND GLU 139 AND THR 141 AND ALA 142, RESPECTIVELY, ARE OBSERVED IN TWO DISTINCT CONFORMATIONS. THE SIDE CHAINS OF NINE RESIDUES (GLN 66, ARG 101, GLU 107, ARG 130, LYS 134, GLU 139, ARG 169, ILE 180, VAL 181) ARE LESS WELL-DEFINED.

-
Components

#1: Protein TETRANECTIN


Mass: 15136.991 Da / Num. of mol.: 1 / Fragment: RESIDUES 45 - 181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PT7H6 / Production host: Escherichia coli (E. coli) / Strain (production host): DH / References: UniProt: P05452
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 53 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: THE PROTEIN WAS CRYSTALLIZED BY THE HANGING DROP METHOD BY MIXING 4 MICROLITER OF A SOLUTION CONTAINING 5 MG/ML PROTEIN, 0.02 M CACL2, 0.05 M NACL, 0.10 M TRIS-HCL, PH 8.0, WITH 3 MICROLITER ...Details: THE PROTEIN WAS CRYSTALLIZED BY THE HANGING DROP METHOD BY MIXING 4 MICROLITER OF A SOLUTION CONTAINING 5 MG/ML PROTEIN, 0.02 M CACL2, 0.05 M NACL, 0.10 M TRIS-HCL, PH 8.0, WITH 3 MICROLITER RESERVOIR SOLUTION CONTAINING 2.1 M AMMONIUM SULFATE, 5 % ETHANOL., vapor diffusion - hanging drop
Crystal
*PLUS
Density % sol: 60 %
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, hanging drop
Details: Kastrup, J.S., (1997) Acta Crystallogr.,Sect.D, 53, 108.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.86 mg/mlprotein1drop
22.86 %isopropanol1drop
32.0 Mammonium sulfate1drop
42.14 %ethanol1drop
55 %ethanol1reservoir
62.1 Mammonium sulfate1reservoir

-
Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.927
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.927 Å / Relative weight: 1
ReflectionResolution: 2→15 Å / Num. obs: 10723 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 23 Å2 / Rsym value: 0.062 / Net I/σ(I): 11.4
Reflection shellResolution: 2→2.05 Å / Redundancy: 5 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.221 / % possible all: 98.3
Reflection
*PLUS
Rmerge(I) obs: 0.062
Reflection shell
*PLUS
Rmerge(I) obs: 0.221

-
Processing

Software
NameVersionClassification
DENZOdata reduction
CCP4data reduction
AMoREphasing
TNT5Erefinement
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2MSB, ONE MONOMER

2msb


Resolution: 2→25 Å / Isotropic thermal model: TNT BCORREL 1.0 / Cross valid method: A POSTERIORI / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
Details: THE STRUCTURE WAS INITIALLY REFINED TO AN R-VALUE OF 34.7 % USING X-PLOR.
RfactorNum. reflection% reflectionSelection details
Rfree0.26 529 5 %RANDOM
Rwork0.215 ---
all0.218 11061 --
obs0.218 11061 98 %-
Solvent computationSolvent model: MOEWS AND KRETSINGER (J.MOL.BIOL. (1995) 91, 201-228)
Bsol: 292 Å2 / ksol: 0.87 e/Å3
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1066 0 7 66 1139
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01611050.8
X-RAY DIFFRACTIONt_angle_deg2.615021.4
X-RAY DIFFRACTIONt_dihedral_angle_d17.76601
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.017311.5
X-RAY DIFFRACTIONt_gen_planes0.0161584
X-RAY DIFFRACTIONt_it2109510
X-RAY DIFFRACTIONt_nbd0.0262810
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.267
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg17.71
X-RAY DIFFRACTIONt_planar_d0.0171.5
X-RAY DIFFRACTIONt_plane_restr0.0164

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more