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- PDB-2llp: Solution structure of a THP type 1 alpha 1 collagen fragment (772-786) -

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Basic information

Entry
Database: PDB / ID: 2llp
TitleSolution structure of a THP type 1 alpha 1 collagen fragment (772-786)
ComponentsCollagen alpha-1(I) chain
KeywordsSTRUCTURAL PROTEIN / CONTRACTILE PROTEIN / triple helical peptide / Structural Genomics / Structural Proteomics in Europe 2 / SPINE-2
Function / homology
Function and homology information


cellular response to fluoride / collagen type I trimer / cellular response to vitamin E / tooth mineralization / Anchoring fibril formation / Crosslinking of collagen fibrils / collagen biosynthetic process / Collagen chain trimerization / Defective VWF binding to collagen type I / platelet-derived growth factor binding ...cellular response to fluoride / collagen type I trimer / cellular response to vitamin E / tooth mineralization / Anchoring fibril formation / Crosslinking of collagen fibrils / collagen biosynthetic process / Collagen chain trimerization / Defective VWF binding to collagen type I / platelet-derived growth factor binding / bone trabecula formation / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / extracellular matrix structural constituent conferring tensile strength / intramembranous ossification / Extracellular matrix organization / embryonic skeletal system development / cartilage development involved in endochondral bone morphogenesis / Collagen biosynthesis and modifying enzymes / skin morphogenesis / collagen-activated tyrosine kinase receptor signaling pathway / endochondral ossification / Platelet Adhesion to exposed collagen / cellular response to fibroblast growth factor stimulus / collagen fibril organization / negative regulation of cell-substrate adhesion / response to steroid hormone / face morphogenesis / Scavenging by Class A Receptors / Assembly of collagen fibrils and other multimeric structures / MET activates PTK2 signaling / Syndecan interactions / GP1b-IX-V activation signalling / skin development / blood vessel development / RUNX2 regulates osteoblast differentiation / Platelet Aggregation (Plug Formation) / Collagen degradation / Non-integrin membrane-ECM interactions / protein localization to nucleus / ECM proteoglycans / response to hyperoxia / Integrin cell surface interactions / positive regulation of epithelial to mesenchymal transition / response to mechanical stimulus / cellular response to retinoic acid / GPVI-mediated activation cascade / cellular response to transforming growth factor beta stimulus / response to cAMP / cellular response to epidermal growth factor stimulus / visual perception / extracellular matrix organization / ossification / secretory granule / skeletal system development / Cell surface interactions at the vascular wall / cellular response to glucose stimulus / cellular response to amino acid stimulus / sensory perception of sound / response to insulin / response to hydrogen peroxide / cellular response to mechanical stimulus / osteoblast differentiation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of canonical Wnt signaling pathway / protein transport / cellular response to tumor necrosis factor / response to estradiol / protease binding / collagen-containing extracellular matrix / positive regulation of cell migration / response to xenobiotic stimulus / endoplasmic reticulum lumen / positive regulation of DNA-templated transcription / extracellular space / extracellular region / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
Fibrillar collagen, C-terminal / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / : / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain ...Fibrillar collagen, C-terminal / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / : / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / Collagen triple helix repeat / Collagen triple helix repeat (20 copies)
Similarity search - Domain/homology
Collagen alpha-1(I) chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, minimisation
Model detailsfewest violations, model 1
AuthorsBertini, I. / Fragai, M. / Luchinat, C. / Melikian, M. / Toccafondi, M. / Lauer, J.L. / Fields, G.B. / Structural Proteomics in Europe 2 (SPINE-2)
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Structural basis for matrix metalloproteinase 1-catalyzed collagenolysis.
Authors: Bertini, I. / Fragai, M. / Luchinat, C. / Melikian, M. / Toccafondi, M. / Lauer, J.L. / Fields, G.B.
History
DepositionNov 15, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_keywords / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.SG_entry / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_keywords.text / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Collagen alpha-1(I) chain
B: Collagen alpha-1(I) chain
C: Collagen alpha-1(I) chain


Theoretical massNumber of molelcules
Total (without water)4,9743
Polymers4,9743
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)30 / 900structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Collagen alpha-1(I) chain / Alpha-1 type I collagen


Mass: 1657.892 Da / Num. of mol.: 3 / Fragment: UNP residues 949-965 / Source method: obtained synthetically / Details: synthesis from Fmoc solid-phase chemistry / Source: (synth.) Homo sapiens (human) / References: UniProt: P02452

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1212D 1H-15N HSQC
1313D HNCA
1413D CBCA(CO)NH
1513D HN(CA)CB

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Sample preparation

DetailsContents: 0.4-0.8 mM [U-98% 13C; U-98% 15N] THP type I collagen, 150 mM sodium chloride, 10 mM calcium chloride, 0.1 mM zinc chloride, 20 mM [U-2H] tris buffer, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMTHP type I collagen-1[U-98% 13C; U-98% 15N]0.4-0.81
150 mMsodium chloride-21
10 mMcalcium chloride-31
0.1 mMzinc chloride-41
20 mMtris buffer-5[U-2H]1
Sample conditionsIonic strength: 0.15 / pH: 7.2 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE9002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2Guntert P.structure solution
CYANA2Guntert P.refinement
Amber8Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
RefinementMethod: simulated annealing, minimisation / Software ordinal: 1
Details: Annealing and structure calculation from constraints, minimisation by using AMBER force field and keeping the constraints
NMR constraintsNOE constraints total: 307 / NOE intraresidue total count: 125 / NOE long range total count: 103 / NOE medium range total count: 1 / NOE sequential total count: 78 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 17 / Protein phi angle constraints total count: 17 / Protein psi angle constraints total count: 17
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 900 / Conformers submitted total number: 30

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