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- PDB-6jec: Structure of a triple-helix region of human collagen type II -

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Basic information

Entry
Database: PDB / ID: 6jec
TitleStructure of a triple-helix region of human collagen type II
Componentshuman collagen type IIType II collagen
KeywordsSTRUCTURAL PROTEIN / collagen
Function / homology
Function and homology information


collagen type I trimer / protein heterotrimerization / Anchoring fibril formation / Crosslinking of collagen fibrils / extracellular matrix assembly / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / platelet-derived growth factor binding / collagen metabolic process / Extracellular matrix organization ...collagen type I trimer / protein heterotrimerization / Anchoring fibril formation / Crosslinking of collagen fibrils / extracellular matrix assembly / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / platelet-derived growth factor binding / collagen metabolic process / Extracellular matrix organization / Collagen biosynthesis and modifying enzymes / skin morphogenesis / Platelet Adhesion to exposed collagen / Scavenging by Class A Receptors / collagen fibril organization / odontogenesis / extracellular matrix structural constituent / Assembly of collagen fibrils and other multimeric structures / MET activates PTK2 signaling / Syndecan interactions / GP1b-IX-V activation signalling / blood vessel development / bone mineralization / SMAD binding / Platelet Aggregation (Plug Formation) / Rho protein signal transduction / Collagen degradation / Non-integrin membrane-ECM interactions / ECM proteoglycans / Integrin cell surface interactions / GPVI-mediated activation cascade / extracellular matrix organization / transforming growth factor beta receptor signaling pathway / skeletal system development / cellular response to amino acid stimulus / Cell surface interactions at the vascular wall / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / regulation of blood pressure / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / protein-macromolecule adaptor activity / collagen-containing extracellular matrix / Interleukin-4 and Interleukin-13 signaling / protease binding / endoplasmic reticulum lumen / extracellular space / extracellular exosome / extracellular region / identical protein binding / metal ion 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 / Collagen triple helix repeat / Collagen triple helix repeat (20 copies)
Similarity search - Domain/homology
Collagen alpha-2(I) chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.049 Å
AuthorsYang, X. / Zhu, Y. / Ye, S. / Zhang, R.
CitationJournal: To Be Published
Title: Structure of a triple-helix region of human collagen type II.
Authors: Yang, X. / Zhu, Y. / Ye, S. / Zhang, R. / Lu, L.
History
DepositionFeb 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: human collagen type II
B: human collagen type II
C: human collagen type II


Theoretical massNumber of molelcules
Total (without water)8,2203
Polymers8,2203
Non-polymers00
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-29 kcal/mol
Surface area5530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)19.360, 22.990, 39.909
Angle α, β, γ (deg.)102.76, 92.14, 113.97
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide human collagen type II / Type II collagen


Mass: 2739.927 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P08123*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 1.91 Å3/Da / Density % sol: 35.47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.2M Sodium Acetate 20%(w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.049→20.294 Å / Num. obs: 3550 / % possible obs: 92.79 % / Redundancy: 4.1 % / Net I/σ(I): 31.6
Reflection shellResolution: 2.05→2.09 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.049→20.294 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 2.16 / Phase error: 16.99
RfactorNum. reflection% reflection
Rfree0.2156 196 5.52 %
Rwork0.1786 --
obs0.1806 3550 92.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.049→20.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms573 0 0 127 700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004612
X-RAY DIFFRACTIONf_angle_d1.331850
X-RAY DIFFRACTIONf_dihedral_angle_d6.629371
X-RAY DIFFRACTIONf_chiral_restr0.09281
X-RAY DIFFRACTIONf_plane_restr0.008118
LS refinement shellResolution: 2.049→2.09 Å
RfactorNum. reflection% reflection
Rfree0.2156 196 -
Rwork0.1786 3354 -
obs--93 %
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)
10.00470.0224-0.02840.274-0.32390.47660.00910.0021-0.08160.07850.0655-0.09490.07060.07890.377-0.03910.0213-0.07280.06490.01890.11893.589737.16735.4479
21.00080.4285-0.29743.3179-0.72260.5270.05270.04710.08590.00740.01530.08-0.0211-0.09830.03820.04220.0008-0.01160.0448-0.00750.06180.36759.112-8.6152
30.6435-0.30590.19860.24630.02360.6319-0.01260.0411-0.0836-0.02620.02710.03320.13690.00820.00020.06890.0140.06190.0077-0.00790.12380.632173.8975-9.0802
40.52940.0381-0.1071.18040.41590.96850.0561-0.00730.0003-0.00190.0673-0.097-0.07810.13070.14230.1215-0.02740.00390.0658-0.00060.05085.413689.1483-15.04
50.44420.451-0.38613.0309-1.30121.20110.12-0.0438-0.01020.18150.0061-0.0227-0.14990.03240.05540.08910.0122-0.04840.0761-0.01310.12170.864334.71837.8362
60.3939-0.28890.07220.48570.09410.0916-0.01770.0751-0.0214-0.0430.050.002-0.07180.04040.0380.12050.0050.02290.07720.01390.05394.322664.585-8.3335
72.03590.0130.06640.31-0.41061.5952-0.01970.09570.2432-0.04150.05050.0008-0.0990.06820.0180.0622-0.0932-0.023-0.0176-0.16550.0370.578486.5631-17.3082
81.0073-1.07791.06765.0963-3.69833.6962-0.0256-0.0944-0.09910.1017-0.0894-0.06740.16840.26380.07740.1975-0.00620.03440.28340.07210.11484.330226.00549.2487
90.05730.108-0.11361.7444-0.77880.42670.0216-0.1264-0.00190.05640.01350.0950.0013-0.0994-0.02090.1256-0.08840.16950.05610.07640.0232-0.949441.60341.3952
100.80650.61050.02063.06080.08281.45880.0494-0.0673-0.01240.0948-0.0003-0.0151-0.0162-0.1880.01240.19020.0846-0.00720.16420.0006-0.0144-0.078858.7299-1.6532
110.2632-0.2090.16970.95060.15510.5799-0.0110.0224-0.0695-0.08480.1043-0.1206-0.19150.08170.06170.0558-0.0021-0.03960.0521-0.01480.0785.333180.9056-14.6474
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 12 )
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 17 )
3X-RAY DIFFRACTION3chain 'A' and (resid 18 through 22 )
4X-RAY DIFFRACTION4chain 'A' and (resid 24 through 28 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 13 )
6X-RAY DIFFRACTION6chain 'B' and (resid 14 through 24 )
7X-RAY DIFFRACTION7chain 'B' and (resid 25 through 30 )
8X-RAY DIFFRACTION8chain 'C' and (resid 0 through 6 )
9X-RAY DIFFRACTION9chain 'C' and (resid 7 through 12 )
10X-RAY DIFFRACTION10chain 'C' and (resid 13 through 17 )
11X-RAY DIFFRACTION11chain 'C' and (resid 18 through 30 )

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