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- PDB-8yv3: The heterotrimer structure of peptides derived from human collage... -

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Basic information

Entry
Database: PDB / ID: 8yv3
TitleThe heterotrimer structure of peptides derived from human collagen type I
Components
  • Collagen alpha-1(I) chain
  • Collagen alpha-2(I) chain
KeywordsSTRUCTURAL PROTEIN / collagen
Function / homology
Function and homology information


collagen type I trimer / cellular response to vitamin E / tooth mineralization / protein heterotrimerization / cellular response to fluoride / Anchoring fibril formation / Crosslinking of collagen fibrils / collagen biosynthetic process / extracellular matrix assembly / Collagen chain trimerization ...collagen type I trimer / cellular response to vitamin E / tooth mineralization / protein heterotrimerization / cellular response to fluoride / Anchoring fibril formation / Crosslinking of collagen fibrils / collagen biosynthetic process / extracellular matrix assembly / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / Defective VWF binding to collagen type I / platelet-derived growth factor binding / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / bone trabecula formation / 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 / cartilage development involved in endochondral bone morphogenesis / Collagen biosynthesis and modifying enzymes / skin morphogenesis / collagen metabolic process / collagen-activated tyrosine kinase receptor signaling pathway / endochondral ossification / Platelet Adhesion to exposed collagen / collagen fibril organization / face morphogenesis / response to steroid hormone / odontogenesis / Assembly of collagen fibrils and other multimeric structures / extracellular matrix structural constituent / MET activates PTK2 signaling / Scavenging by Class A Receptors / GP1b-IX-V activation signalling / Syndecan interactions / blood vessel development / bone mineralization / SMAD binding / RUNX2 regulates osteoblast differentiation / Platelet Aggregation (Plug Formation) / Collagen degradation / Non-integrin membrane-ECM interactions / cellular response to fibroblast growth factor stimulus / negative regulation of cell-substrate adhesion / protein localization to nucleus / Rho protein signal transduction / ECM proteoglycans / response to hyperoxia / Integrin cell surface interactions / positive regulation of epithelial to mesenchymal transition / response to cAMP / cellular response to transforming growth factor beta stimulus / GPVI-mediated activation cascade / cellular response to retinoic acid / visual perception / transforming growth factor beta receptor signaling pathway / cellular response to epidermal growth factor stimulus / secretory granule / skeletal system development / Cell surface interactions at the vascular wall / response to insulin / cellular response to amino acid stimulus / sensory perception of sound / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / cellular response to glucose stimulus / response to hydrogen peroxide / regulation of blood pressure / cellular response to mechanical stimulus / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / 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 / : / Interleukin-4 and Interleukin-13 signaling / positive regulation of cell migration / endoplasmic reticulum lumen / response to xenobiotic stimulus / positive regulation of DNA-templated transcription / extracellular space / extracellular exosome / extracellular region / metal ion binding / identical protein binding
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsZhu, Y. / Yang, X. / Sun, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The heterotrimer structure of peptides derived from human collagen type I
Authors: Zhu, Y. / Yang, X. / Sun, F.
History
DepositionMar 27, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Collagen alpha-1(I) chain
B: Collagen alpha-2(I) chain
C: Collagen alpha-2(I) chain
D: Collagen alpha-1(I) chain
E: Collagen alpha-2(I) chain
F: Collagen alpha-2(I) chain


Theoretical massNumber of molelcules
Total (without water)17,6436
Polymers17,6436
Non-polymers00
Water5,513306
1
A: Collagen alpha-1(I) chain
B: Collagen alpha-2(I) chain
C: Collagen alpha-2(I) chain


Theoretical massNumber of molelcules
Total (without water)8,8223
Polymers8,8223
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-19 kcal/mol
Surface area5690 Å2
MethodPISA
2
D: Collagen alpha-1(I) chain
E: Collagen alpha-2(I) chain
F: Collagen alpha-2(I) chain


Theoretical massNumber of molelcules
Total (without water)8,8223
Polymers8,8223
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-23 kcal/mol
Surface area6090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.490, 33.043, 38.519
Angle α, β, γ (deg.)82.17, 77.73, 69.64
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 2933.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P02452
#2: Protein/peptide
Collagen alpha-2(I) chain / Alpha-2 type I collagen


Mass: 2944.246 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P08123
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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 Å3/Da / Density % sol: 38.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium Sulfate. 0.1 M Tris:HCI pH 8.5 25%(w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: CCD / Date: Jan 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.68→30.91 Å / Num. obs: 11231 / % possible obs: 71.65 % / Redundancy: 3.8 % / CC1/2: 0.998 / Net I/σ(I): 19.86
Reflection shellResolution: 1.68→1.74 Å / Num. unique obs: 220 / CC1/2: 0.81

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→30.91 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 27.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2332 530 4.72 %
Rwork0.1935 --
obs0.1954 11222 71.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.68→30.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1234 0 0 306 1540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041286
X-RAY DIFFRACTIONf_angle_d0.7561714
X-RAY DIFFRACTIONf_dihedral_angle_d13.037216
X-RAY DIFFRACTIONf_chiral_restr0.041149
X-RAY DIFFRACTIONf_plane_restr0.009251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.850.3815330.2796861X-RAY DIFFRACTION23
1.85-2.120.26971340.2162758X-RAY DIFFRACTION74
2.12-2.670.25521880.20143472X-RAY DIFFRACTION94
2.67-30.910.19871750.17533601X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3741-0.4980.08961.72630.38250.3868-0.05140.03810.0332-0.15450.0461-0.111-0.0680.1287-0.08880.00060.00860.03460.1140.03030.082238.129110.737419.4913
21.0141-0.9556-0.33626.48793.35142.5727-0.08460.0622-0.10440.14570.0616-0.13850.21130.3418-0.06960.10510.00140.0150.1481-0.0130.113448.3672-19.494410.4886
30.0755-0.3689-0.06672.33760.32620.0577-0.02320.3215-0.4999-0.39390.1937-0.04980.51550.1609-0.03860.31980.05340.0940.2489-0.04240.272152.5452-38.32851.0939
40.7584-0.822-0.48742.89960.97140.8698-0.0516-0.14450.00670.13250.11450.09350.0640.0961-0.08180.044-0.020.00330.0944-0.00550.068333.923121.673125.4016
51.539-2.3958-1.32124.94712.0261.1265-0.13060.1872-0.07530.02130.08090.1657-0.07080.0260.05030.06930.0274-0.01660.1016-0.00120.069740.992-6.077815.2785
62.5616-0.5969-1.58176.92332.72783.25650.25910.2078-0.0575-0.22770.0680.3509-0.3327-0.10330.14580.2392-0.0050.00190.11270.00480.103149.5285-24.74171.9294
76.795-1.441-1.53055.87181.90776.5553-0.0283-0.0083-0.2711-0.11420.0512-0.19070.1970.33040.03120.24220.0230.03360.1187-0.01280.096857.6878-34.5954-0.2027
81.1883-2.0839-0.91954.55531.77421.397-0.057-0.1556-0.0418-0.00850.1416-0.0146-0.06590.0367-0.09740.055-0.0016-0.01490.09160.03240.100232.497916.170423.5139
92.1107-3.6782-0.9277.62712.34160.84070.10770.18780.2616-0.44820.136-0.3627-0.30390.0994-0.16780.1319-0.05720.01390.1090.02610.107345.7306-6.339310.2265
100.9816-1.693-0.22384.35261.80151.4529-0.01490.03690.1078-0.83190.0356-0.41960.27650.1437-0.20730.2281-0.01750.07570.1916-0.01640.140753.6709-21.34715.8788
114.4461-4.581-2.25217.48171.55621.3517-0.0905-0.0897-0.0436-0.2181-0.1068-0.19830.24710.1581-0.18220.23080.0263-0.0260.1856-0.02830.083955.5201-34.11875.5078
120.1447-0.2988-0.07642.00761.2710.92810.0348-0.0006-0.03340.0578-0.21140.10610.1075-0.2117-0.19930.4647-0.07440.17510.1411-0.11930.016563.2229-24.07136.2331
131.1325-1.2378-0.43283.13810.90280.8187-0.08710.0967-0.0892-0.0073-0.09830.10010.08990.03460.00530.0601-0.0120.03530.0562-0.00950.067859.4067-5.654218.137
141.1519-1.75610.58636.8436-0.31750.38-0.1213-0.02740.06110.05990.1966-0.4114-0.01790.0359-0.07110.10020.0055-0.03040.0695-0.00810.083953.753314.054422.4652
152.4971-1.6372-0.78353.23430.3352.0174-0.04450.11150.40890.17520.1003-0.2969-0.325-0.0207-0.10520.0233-0.0437-0.0580.1160.01650.116542.234932.311427.0191
161.4821-1.7624-0.98553.72721.72911.47770.1630.12450.0135-0.1524-0.1104-0.01270.0857-0.05160.01980.12080.0119-0.03950.10490.00630.046159.6198-8.967513.431
171.8196-0.8326-0.63727.76092.44721.1837-0.1566-0.14590.07670.4997-0.03810.21660.22640.19010.00050.150.0276-0.00190.12660.01370.059445.461826.360931.1288
181.0605-0.6141-0.40943.76820.51560.7428-0.1462-0.0535-0.22420.07940.07620.37480.24570.09380.01580.62850.019-0.11920.12290.02190.28567.0021-26.88289.8216
192.2064-3.3059-1.49385.21622.00761.18590.19490.1736-0.0089-0.3424-0.24730.1683-0.1262-0.08250.04150.0981-0.0433-0.00290.1229-0.00660.116557.22750.901215.4837
202.2591-1.9972-0.72723.33511.57131.9654-0.2346-0.0072-0.2570.34180.28650.1308-0.0682-0.08590.03630.15240.00670.04350.11410.00860.113340.311427.782330.1689
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 15 )
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 25 )
3X-RAY DIFFRACTION3chain 'A' and (resid 26 through 29 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 10 )
5X-RAY DIFFRACTION5chain 'B' and (resid 11 through 21 )
6X-RAY DIFFRACTION6chain 'B' and (resid 22 through 26 )
7X-RAY DIFFRACTION7chain 'B' and (resid 27 through 30 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 15 )
9X-RAY DIFFRACTION9chain 'C' and (resid 16 through 21 )
10X-RAY DIFFRACTION10chain 'C' and (resid 22 through 26 )
11X-RAY DIFFRACTION11chain 'C' and (resid 27 through 30 )
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 5 )
13X-RAY DIFFRACTION13chain 'D' and (resid 6 through 15 )
14X-RAY DIFFRACTION14chain 'D' and (resid 16 through 20 )
15X-RAY DIFFRACTION15chain 'D' and (resid 21 through 30 )
16X-RAY DIFFRACTION16chain 'E' and (resid 1 through 21 )
17X-RAY DIFFRACTION17chain 'E' and (resid 22 through 30 )
18X-RAY DIFFRACTION18chain 'F' and (resid 1 through 5 )
19X-RAY DIFFRACTION19chain 'F' and (resid 6 through 21 )
20X-RAY DIFFRACTION20chain 'F' and (resid 22 through 30 )

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