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- PDB-3hr2: Low resolution, molecular envelope structure of type I collagen i... -

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Basic information

Entry
Database: PDB / ID: 3hr2
TitleLow resolution, molecular envelope structure of type I collagen in situ determined by fiber diffraction. Single type I collagen molecule, post rigid body refinement, 'relaxed'
Components
  • Collagen alpha-1(I) chain
  • Collagen alpha-2(I) chain
KeywordsSTRUCTURAL PROTEIN / CONTRACTILE PROTEIN / NATIVE / IN SITU / Molecular envelope / TRIPLE-helical / SUPERMOLECULAR / supramolecular / PACKING STRUCTURE / STRUCTURAL PROTEIN-CONTRACTILE PROTEIN COMPLEX / Collagen / Extracellular matrix / Glycoprotein / Hydroxylation / Pyrrolidone carboxylic acid / Secreted
Function / homology
Function and homology information


cellular response to aldehyde / Extracellular matrix organization / Collagen biosynthesis and modifying enzymes / Crosslinking of collagen fibrils / Non-integrin membrane-ECM interactions / Platelet Aggregation (Plug Formation) / Collagen chain trimerization / response to norepinephrine / MET activates PTK2 signaling / GP1b-IX-V activation signalling ...cellular response to aldehyde / Extracellular matrix organization / Collagen biosynthesis and modifying enzymes / Crosslinking of collagen fibrils / Non-integrin membrane-ECM interactions / Platelet Aggregation (Plug Formation) / Collagen chain trimerization / response to norepinephrine / MET activates PTK2 signaling / GP1b-IX-V activation signalling / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / Integrin cell surface interactions / Platelet Adhesion to exposed collagen / response to fluoride / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / GPVI-mediated activation cascade / ECM proteoglycans / Cell surface interactions at the vascular wall / collagen type I trimer / cellular response to vitamin E / tooth mineralization / protein heterotrimerization / cellular response to fluoride / collagen biosynthetic process / extracellular matrix assembly / extracellular matrix structural constituent conferring tensile strength / platelet-derived growth factor binding / bone trabecula formation / intramembranous ossification / embryonic skeletal system development / cartilage development involved in endochondral bone morphogenesis / skin morphogenesis / collagen metabolic process / collagen-activated tyrosine kinase receptor signaling pathway / endochondral ossification / collagen trimer / cellular response to thyroid hormone stimulus / collagen fibril organization / face morphogenesis / response to steroid hormone / skeletal system morphogenesis / extracellular matrix structural constituent / skin development / blood vessel development / bone mineralization / SMAD binding / cellular response to fibroblast growth factor stimulus / negative regulation of cell-substrate adhesion / protein localization to nucleus / Rho protein signal transduction / response to hyperoxia / positive regulation of epithelial to mesenchymal transition / response to mechanical stimulus / response to cAMP / cellular response to transforming growth factor beta stimulus / cellular response to retinoic acid / response to nutrient / visual perception / extracellular matrix / transforming growth factor beta receptor signaling pathway / cellular response to epidermal growth factor stimulus / ossification / secretory granule / skeletal system development / response to insulin / cellular response to amino acid stimulus / sensory perception of sound / response to nutrient levels / cellular response to glucose stimulus / : / response to hydrogen peroxide / regulation of blood pressure / response to peptide hormone / cellular response to mechanical stimulus / osteoblast differentiation / positive regulation of canonical Wnt signaling pathway / protein transport / cellular response to tumor necrosis factor / response to estradiol / protease binding / protein-macromolecule adaptor activity / : / positive regulation of cell migration / response to xenobiotic stimulus / positive regulation of DNA-templated transcription / extracellular space / extracellular region / metal ion binding / identical protein 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 / Collagen alpha-2(I) chain
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodFIBER DIFFRACTION / SYNCHROTRON / MIR / Resolution: 5.16 Å
AuthorsOrgel, J.P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: Microfibrillar Structure of Type I Collagen in Situ.
Authors: Orgel, J.P. / Irving, T.C. / Miller, A. / Wess, T.J.
History
DepositionJun 8, 2009Deposition site: RCSB / Processing site: RCSB
SupersessionJul 14, 2009ID: 1Y0F
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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-2(I) chain
C: Collagen alpha-1(I) chain


Theoretical massNumber of molelcules
Total (without water)286,9763
Polymers286,9763
Non-polymers00
Water00
1
A: Collagen alpha-1(I) chain
B: Collagen alpha-2(I) chain
C: Collagen alpha-1(I) chain
x 9


Theoretical massNumber of molelcules
Total (without water)2,582,78427
Polymers2,582,78427
Non-polymers00
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation1_151x-4,y,z-41
crystal symmetry operation1_252x-3,y,z-31
crystal symmetry operation1_353x-2,y,z-21
crystal symmetry operation1_454x-1,y,z-11
crystal symmetry operation1_555x,y,z1
crystal symmetry operation1_656x+1,y,z+11
crystal symmetry operation1_757x+2,y,z+21
crystal symmetry operation1_858x+3,y,z+31
crystal symmetry operation1_959x+4,y,z+41
Unit cell
Length a, b, c (Å)39.97, 26.95, 677.9
Angle α, β, γ (deg.)89.24, 94.59, 105.58
Int Tables number1
Space group name H-MP1
DetailsBIOMOLECULE: THIS ENTRY CONTAINS ONE COLLAGEN TYPE I MOLECULE. FOR RELATION TO THE FIBRILLAR PACKING OF COLLAGEN MOLECULES/MICRO-FIBRIL, REFER TO CITATION. IN SUMMARY: EACH COLLAGEN MOLECULE IS STAGGERED BY AN INTEGER MULTIPLE OF THE C-CELL AXIS. THE STRUCTURE CAN BE EXTENDED IN THE AXIAL (~C-CELL AXIS) DIRECTION BY APPLYING THE FOLLOWING TRANSLATION: NX,0Y,NZ TO THE MOLECULE, WHERE N IS AN INTEGER. A VISUALIZATION OF FIVE SUCCESSIVE 'D'-REPEATS OF THE BIOMOLECULE / MICRO-FIBRIL CAN BE OBTAINED FROM THESE COORDINATES BY APPLYING THE FOLLOWING TRANSLATIONS TO NINE COORDINATE SETS: A) 0, 0, 0; B) -1, 0,-1; C) -2, 0,-2; D) -3, 0,-3; E) -4, 0,-4; B1) 1, 0, 1; C1) 2, 0, 2; D1) 3, 0, 3; E1) 4, 0, 4.

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Components

#1: Protein Collagen alpha-1(I) chain / Alpha-1 type I collagen / Coordinate model: Cα atoms only


Mass: 96747.344 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Tissue: tail tendon / References: UniProt: P02454
#2: Protein Collagen alpha-2(I) chain / Alpha-2 type I collagen / Coordinate model: Cα atoms only


Mass: 93481.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Tissue: tail tendon / References: UniProt: P02466

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Experimental details

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Experiment

ExperimentMethod: FIBER DIFFRACTION / Number of used crystals: 6

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Sample preparation

CrystalDescription: THE RESOLUTION LIMITS FOR THE DATA COLLECTION ARE 38.5 TO 11.1A LATERAL AND 112.6 TO 5.16A AXIAL, INTENSITY-INTEGRATION SOFTWARE : FIT2D/IN-HOUSE, DATA SCALING SOFTWARE : IN-HOUSE

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 18-ID / Wavelength: 1.03
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Nov 15, 1998 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 5.16→112.6 Å / Num. all: 436 / Num. obs: 424 / % possible obs: 97 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 5.16→112.6 Å / % possible all: 97

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Processing

SoftwareName: CNS / Classification: refinement
RefinementMethod to determine structure: MIR / Resolution: 5.16→112.62 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
Details: 305 EQUATORIAL AND 109 MERIDIONAL REFLECTIONS WERE USED FOR REFINEMENT WITH CNS. INITIAL REFINEMENT OF WHOLE MOLECULAR PATHS WAS PERFORMED IN THE STEPWISE FASHION DESCRIBED IN THE CITED ...Details: 305 EQUATORIAL AND 109 MERIDIONAL REFLECTIONS WERE USED FOR REFINEMENT WITH CNS. INITIAL REFINEMENT OF WHOLE MOLECULAR PATHS WAS PERFORMED IN THE STEPWISE FASHION DESCRIBED IN THE CITED PUBLICATION. MODEL STRUCTURE FACTORS WHERE INITIALLY GENERATED FROM THE WHOLE RESIDUE SCATTERING FACTORS OF HULMES ET AL 1977 WHICH WERE SUBSTITUTED FOR THE CALPHA POSITIONS AND THE SQUARE FC'S WERE CALCULATED FOR COMPARISON BETWEEN A SIMULATED DIFFRACTION PATTERN AND THE OBSERVED PATTERNS. STRUCTURE FACTORS FROM THE FINAL MODEL WERE GENERATED IN THE NORMAL MANNER FOR REFINEMENT OF THE TELOPEPTIDE CONFORMATIONS USING CNS (SEE ABOVE). TWO ROUNDS OF Q-FACTOR REFINEMENT FOLLOWED BY ONE ROUND OF CONSTRAINED THEN UNCONSTRAINED ANNEALING FOR THE WHOLE STRUCTURE. THE R- FACTOR WHEN MEASURED VIA SIMULATED/OBSERVED DIFFRACTION PATTERN COMPARISON WAS FOUND TO BE 16.7% AND 6.6% BY MEASURE OF THE INTERGRATED STRUCTURE FACTORS. REFLECTIONS MISSING FROM THE MERIDONAL(OOL) SERIES WERE EITHER TOO WEAK TO MEASURE AND/OR VAIRED SIGNIFICANTLY BETWEEN COLLECTED PATTERNS (SEVEN IN TOTAL). THE FIRST FIVE REFLECTIONS WHERE EXCLUDED DUE TO THEIR LOW RESOLUTION (677.9 TO ~120 ANGSTROMS). EXLUDED REFLECTIONS ARE NOT INCLUDED IN THE 414 TOTAL. THE COORDINATES CONTAIN CA ATOMS ONLY.
RfactorNum. reflection% reflectionSelection details
Rwork0.042 ---
obs0.042 424 97 %-
all-436 --
Rfree---See details
Refinement stepCycle: LAST / Resolution: 5.16→112.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3134 0 0 0 3134

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