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- PDB-1aq5: HIGH-RESOLUTION SOLUTION NMR STRUCTURE OF THE TRIMERIC COILED-COI... -

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Basic information

Entry
Database: PDB / ID: 1aq5
TitleHIGH-RESOLUTION SOLUTION NMR STRUCTURE OF THE TRIMERIC COILED-COIL DOMAIN OF CHICKEN CARTILAGE MATRIX PROTEIN, 20 STRUCTURES
ComponentsCARTILAGE MATRIX PROTEIN
KeywordsCOILED-COIL / HEPTAD REPEAT / INTERCHAIN DISULFIDE BONDS / OLIGOMERIZATION DOMAIN / TRIMER / CARTILAGE MATRIX PROTEIN / MATRILIN-1 / NONCOLLAGENOUS EXTRACELLULAR PROTEIN
Function / homology
Function and homology information


: / calcium ion binding / extracellular region
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #30 / Matrilin, coiled-coil trimerisation domain / Matrilin, coiled-coil domain superfamily / Trimeric coiled-coil oligomerisation domain of matrilin / Trimeric coiled-coil oligomerisation domain of matrilin / : / von Willebrand factor type A domain / Coagulation Factor Xa inhibitory site / VWFA domain profile. / von Willebrand factor (vWF) type A domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #30 / Matrilin, coiled-coil trimerisation domain / Matrilin, coiled-coil domain superfamily / Trimeric coiled-coil oligomerisation domain of matrilin / Trimeric coiled-coil oligomerisation domain of matrilin / : / von Willebrand factor type A domain / Coagulation Factor Xa inhibitory site / VWFA domain profile. / von Willebrand factor (vWF) type A domain / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / von Willebrand factor, type A / Epidermal growth factor-like domain. / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / EGF-like domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsDames, S.A. / Wiltscheck, R. / Kammerer, R.A. / Engel, J. / Alexandrescu, A.T.
Citation
Journal: Nat.Struct.Biol. / Year: 1998
Title: NMR structure of a parallel homotrimeric coiled coil.
Authors: Dames, S.A. / Kammerer, R.A. / Wiltscheck, R. / Engel, J. / Alexandrescu, A.T.
#1: Journal: Protein Sci. / Year: 1997
Title: Heteronuclear NMR assignments and secondary structure of the coiled coil trimerization domain from cartilage matrix protein in oxidized and reduced forms.
Authors: Wiltscheck, R. / Kammerer, R.A. / Dames, S.A. / Schulthess, T. / Blommers, M.J. / Engel, J. / Alexandrescu, A.T.
History
DepositionAug 7, 1997Processing site: BNL
Revision 1.0Feb 11, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 13, 2021Group: Other / Structure summary / Category: entity / pdbx_database_status / Item: _entity.details / _pdbx_database_status.process_site
Revision 1.4Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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: CARTILAGE MATRIX PROTEIN
B: CARTILAGE MATRIX PROTEIN
C: CARTILAGE MATRIX PROTEIN


Theoretical massNumber of molelcules
Total (without water)16,1803
Polymers16,1803
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 30LOWEST ENERGY AND LEAST RESTRAINT VIOLATIONS
Representative

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Components

#1: Protein/peptide CARTILAGE MATRIX PROTEIN / MATRILIN-1 / CMP


Mass: 5393.254 Da / Num. of mol.: 3
Fragment: CMPCC, COILED-COIL OLIGOMERIZATION DOMAIN, RESIDUES 451 - 493
Mutation: INS(GSHM) AT THE N-TERMINUS OF THE COILED-COIL DOMAIN
Source method: isolated from a genetically manipulated source
Details: INTERCHAIN DISULFIDE BONDS / Source: (gene. exp.) Gallus gallus (chicken) / Tissue: CARTILAGE MATRIX / Cell line: BL21 / Gene: CMP / Plasmid: BL21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P05099
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1312D 1H-15N HSQC
1412D 1H-13C HSQC
1513D 1H-15N NOESY-HSQC
1613D 1H-15N TOCSY-HSQC
1713D (H)CCH-TOCSY
1813D HNCA
1913D HNHA
11013D HNHB
11112D VERSION OF A 4D 13C/15N HMQC-NOESY-HMQC
11213D 13C F1-EDITED
1131F3-FILTERED HMQC-NOESY

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Sample preparation

Sample conditionspH: 5.5 / Temperature: 323 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLOR3.1structure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
Details: ALL STRUCTURE CALCULATIONS WERE PERFORMED USING X-PLOR VERSION 3.1. FIRST 60 MONOMER STRUCTURES WERE CALCULATED FROM INTRACHAIN DISTANCE RESTRAINTS, TOGETHER WITH THE DIHEDRAL ANGLE ...Details: ALL STRUCTURE CALCULATIONS WERE PERFORMED USING X-PLOR VERSION 3.1. FIRST 60 MONOMER STRUCTURES WERE CALCULATED FROM INTRACHAIN DISTANCE RESTRAINTS, TOGETHER WITH THE DIHEDRAL ANGLE RESTRAINTS FOR PHI AND CHI1 AND THE HYDROGEN BOND RESTRAINTS, USING THE HYBRID DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD (NILGES, M.; CLORE, G.M.; GRONENBORN, A.M. (1988); FEBS LETT. 229, 317-324). THE 30 BEST MONOMER STRUCTURES WERE USED AS INPUT FOR THE GENERATION OF TRIMER STARTING STRUCTURES. EACH SELECTED HELIX MONOMER WAS FIRST ORIENTED SUCH THAT ITS GEOMETRIC CENTER COINCIDED WITH THE ORIGIN AND ITS LONG AXIS LAY ALONG THE X-AXIS AND SECOND TRANSLATED BY 10 ANGSTROMS ALONG THE Y-AXIS. COORDINATES FOR THE SECOND AND THIRD SUBUNIT WERE GENERATED BY A ROTATION AROUND THE X-AXIS BY 120 OR 240 DEGREES, RESPECTIVELY. THE 30 GENERATED TRIMER STARTING STRUCTURES WERE USED AS INPUT FOR A SECOND RUN OF SIMULATED ANNEALING INCLUDING THE INTERCHAIN DISTANCE RESTRAINTS. IN THE RESULTING STRUCTURES THE INTERCHAIN DISULFIDE BONDS WERE INTRODUCED AND A FINAL RUN OF SIMULATED ANNEALING AND REFINEMENT PERFORMED. THE LAST STEPS OF REFINEMENT INCLUDED ADDITIONALLY NON-CRYSTALLOGRAPHIC SYMMETRY (NCS) CONSTRAINTS AND R^(-6)-SUM AVERAGED DISTANCE RESTRAINTS FOR AMBIGUOUS NOES (NILGES, M. (1993); PROTEINS 17, 297-309).
NMR ensembleConformer selection criteria: LOWEST ENERGY AND LEAST RESTRAINT VIOLATIONS
Conformers calculated total number: 30 / Conformers submitted total number: 20

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