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- PDB-3dmw: Crystal structure of human type III collagen G982-G1023 containin... -

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Basic information

Entry
Database: PDB / ID: 3dmw
TitleCrystal structure of human type III collagen G982-G1023 containing C-terminal cystine knot
ComponentsCollagen alpha-1(III) chain
KeywordsSTRUCTURAL PROTEIN / collagen III / cystine knot / triple helix / glycine / MAD phasing / Alternative splicing / Disease mutation / Ehlers-Danlos syndrome / Extracellular matrix / Glycoprotein / Hydroxylation / Phosphoprotein / Polymorphism / Secreted
Function / homology
Function and homology information


collagen type III trimer / aorta smooth muscle tissue morphogenesis / limb joint morphogenesis / transforming growth factor beta1 production / elastic fiber assembly / negative regulation of neuron migration / Collagen chain trimerization / platelet-derived growth factor binding / endochondral bone morphogenesis / extracellular matrix structural constituent conferring tensile strength ...collagen type III trimer / aorta smooth muscle tissue morphogenesis / limb joint morphogenesis / transforming growth factor beta1 production / elastic fiber assembly / negative regulation of neuron migration / Collagen chain trimerization / platelet-derived growth factor binding / endochondral bone morphogenesis / extracellular matrix structural constituent conferring tensile strength / basement membrane organization / Extracellular matrix organization / layer formation in cerebral cortex / Collagen biosynthesis and modifying enzymes / peptide cross-linking / tissue homeostasis / Signaling by PDGF / negative regulation of immune response / NCAM1 interactions / digestive tract development / response to angiotensin / collagen fibril organization / Scavenging by Class A Receptors / extracellular matrix structural constituent / skin development / MET activates PTK2 signaling / Assembly of collagen fibrils and other multimeric structures / Syndecan interactions / positive regulation of Rho protein signal transduction / SMAD binding / Collagen degradation / Non-integrin membrane-ECM interactions / ECM proteoglycans / Integrin cell surface interactions / chondrocyte differentiation / supramolecular fiber organization / extracellular matrix organization / cell-matrix adhesion / transforming growth factor beta receptor signaling pathway / response to cytokine / integrin-mediated signaling pathway / cellular response to amino acid stimulus / neuron migration / lung development / wound healing / response to radiation / multicellular organism growth / cerebral cortex development / platelet activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / heart development / fibroblast proliferation / collagen-containing extracellular matrix / in utero embryonic development / protease binding / endoplasmic reticulum lumen / extracellular space / extracellular region / 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 / 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(III) chain
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsBoudko, S.P. / Engel, J. / Okuyama, K. / Mizuno, K. / Bachinger, H.P. / Schumacher, M.A.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal structure of human type III collagen Gly991-Gly1032 cystine knot-containing peptide shows both 7/2 and 10/3 triple helical symmetries.
Authors: Boudko, S.P. / Engel, J. / Okuyama, K. / Mizuno, K. / Bachinger, H.P. / Schumacher, M.A.
History
DepositionJul 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)11,9193
Polymers11,9193
Non-polymers00
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6600 Å2
ΔGint-23.1 kcal/mol
Surface area7070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.980, 21.520, 68.970
Angle α, β, γ (deg.)90.00, 92.58, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe peptide assembles into a triple helix (3 chains of the 42-mer)

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Components

#1: Protein/peptide Collagen alpha-1(III) chain


Mass: 3973.109 Da / Num. of mol.: 3 / Fragment: UNP residues 1158-1199 / Mutation: Q1183M / Source method: obtained synthetically
Details: Chemically synthesized peptide G982-G1023 based on the fragment 1158-1199 of the human Collagen alpha-1(III) chain, CO3A1_HUMAN, UniProt entry P02461.
References: UniProt: P02461
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 1.99 Å3/Da / Density % sol: 38.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% PEG 550, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0000, 0.979, 1.02, 0.97963
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 12, 2007 / Details: Mirrors
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.9791
31.021
40.979631
ReflectionResolution: 2.3→34.45 Å / Num. all: 3964 / Num. obs: 3964 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 7.3
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 5 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.3 / Num. unique all: 583 / Rsym value: 0.24 / % possible all: 89

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→34.45 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 843794.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.274 425 10.8 %RANDOM
Rwork0.248 ---
all0.254 3950 --
obs0.248 3949 89.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.5119 Å2 / ksol: 0.354611 e/Å3
Displacement parametersBiso mean: 25.5 Å2
Baniso -1Baniso -2Baniso -3
1--9.64 Å20 Å215.88 Å2
2---7.59 Å20 Å2
3---17.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.3→34.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms740 0 0 61 801
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d18.9
X-RAY DIFFRACTIONc_improper_angle_d1.44
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.347 52 7.7 %
Rwork0.347 623 -
obs-534 93 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep9.paramprotein4.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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