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- PDB-1q7d: Structure of the integrin alpha2beta1 binding collagen peptide -

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Basic information

Entry
Database: PDB / ID: 1q7d
TitleStructure of the integrin alpha2beta1 binding collagen peptide
Componentscollagen alfa 1(I) chain peptide GPOGPOGFOGERGPOGPOGPO
KeywordsCONTRACTILE PROTEIN / COLLAGEN / INTEGRIN / TRIPLEHELIX
Function / homology
Function and homology information


cellular response to fluoride / collagen type I trimer / tooth mineralization / cellular response to vitamin E / collagen type IV trimer / Anchoring fibril formation / Crosslinking of collagen fibrils / collagen biosynthetic process / Collagen chain trimerization / Enhanced cleavage of VWF variant by ADAMTS13 ...cellular response to fluoride / collagen type I trimer / tooth mineralization / cellular response to vitamin E / collagen type IV trimer / Anchoring fibril formation / Crosslinking of collagen fibrils / collagen biosynthetic process / Collagen chain trimerization / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / Defective VWF binding to collagen type I / platelet-derived growth factor binding / bone trabecula formation / extracellular matrix structural constituent conferring tensile strength / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / intramembranous ossification / Extracellular matrix organization / embryonic skeletal system development / Collagen biosynthesis and modifying enzymes / cartilage development involved in endochondral bone morphogenesis / skin morphogenesis / collagen-activated tyrosine kinase receptor signaling pathway / Platelet Adhesion to exposed collagen / endochondral ossification / 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 / skin development / MET activates PTK2 signaling / Assembly of collagen fibrils and other multimeric structures / Syndecan interactions / GP1b-IX-V activation signalling / blood vessel development / RUNX2 regulates osteoblast differentiation / Platelet Aggregation (Plug Formation) / Collagen degradation / protein localization to nucleus / Non-integrin membrane-ECM interactions / 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 epidermal growth factor stimulus / response to cAMP / cellular response to transforming growth factor beta stimulus / visual perception / extracellular matrix organization / ossification / secretory granule / skeletal system development / Cell surface interactions at the vascular wall / cellular response to glucose stimulus / sensory perception of sound / cellular response to amino acid stimulus / response to insulin / response to hydrogen peroxide / osteoblast differentiation / cellular response to mechanical stimulus / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of canonical Wnt signaling pathway / protein transport / response to estradiol / cellular response to tumor necrosis factor / collagen-containing extracellular matrix / protease binding / 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 / Collagen triple helix repeat / Collagen triple helix repeat (20 copies)
Similarity search - Domain/homology
Collagen alpha-1(I) chain
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsEmsley, J. / Knight, C.G. / Farndale, R.W. / Barnes, M.J.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Structure of the Integrin alpha2beta1-binding Collagen Peptide.
Authors: Emsley, J. / Knight, C.G. / Farndale, R.W. / Barnes, M.J.
History
DepositionAug 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 999SEQUENCE The peptide is acetylated at the N-terminus and amidated at the C-terminus. Gly-Pro-Hyp ...SEQUENCE The peptide is acetylated at the N-terminus and amidated at the C-terminus. Gly-Pro-Hyp groups were added for stabilization.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: collagen alfa 1(I) chain peptide GPOGPOGFOGERGPOGPOGPO
B: collagen alfa 1(I) chain peptide GPOGPOGFOGERGPOGPOGPO
C: collagen alfa 1(I) chain peptide GPOGPOGFOGERGPOGPOGPO


Theoretical massNumber of molelcules
Total (without water)6,1183
Polymers6,1183
Non-polymers00
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-20 kcal/mol
Surface area3820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.600, 135.800, 25.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-24-

HOH

21A-113-

HOH

31B-107-

HOH

41B-116-

HOH

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Components

#1: Protein/peptide collagen alfa 1(I) chain peptide GPOGPOGFOGERGPOGPOGPO


Mass: 2039.167 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN HOMO SAPIENS (HUMAN). PEPTIDE SYNTHESISED USING STANDARD FMOC SYNTHESIS
References: UniProt: P02452
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.12 Å3/Da / Density % sol: 41.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 8K, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
20.1 Mcacodylate1reservoirpH6.5
30.2 Msodium acetate1reservoir
430 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 85 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 6, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 5060 / Num. obs: 5060 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 0.8 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 12.9
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 5 / Num. unique all: 689 / Rsym value: 0.355 / % possible all: 95.2
Reflection
*PLUS
% possible obs: 98.2 % / Redundancy: 2.9 % / Rmerge F obs: 0.089
Reflection shell
*PLUS
Rmerge(I) obs: 0.344

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→6 Å / Cross valid method: RFREE / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 265 -5%
Rwork0.2363 ---
obs0.2363 4865 5.4 %-
all-4923 --
Displacement parametersBiso mean: -0.547 Å2
Baniso -1Baniso -2Baniso -3
1--2.434 Å20 Å20 Å2
2--1.375 Å20 Å2
3---1.059 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-6 Å
Luzzati sigma a0.1 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms429 0 0 94 523
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_d1.6
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d9.5
LS refinement shellResolution: 1.8→1.88 Å / Rfactor Rfree error: 0.01
RfactorNum. reflection% reflection
Rfree0.485 22 -
Rwork0.358 --
obs-548 95 %
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.259 / Rfactor Rwork: 0.236
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0074
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.61
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg9.5

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