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- PDB-4aej: Crystal structure of Human fibrillar procollagen type III C- prop... -

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Basic information

Entry
Database: PDB / ID: 4aej
TitleCrystal structure of Human fibrillar procollagen type III C- propeptide trimer
ComponentsCOLLAGEN ALPHA-1(III) CHAIN
KeywordsSTRUCTURAL PROTEIN / EXTRACELLULAR / MATRIX / FIBROSIS / TRIMER
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
Transcription Regulator spoIIAA - #130 / Jelly Rolls - #1000 / Fibrillar collagen, C-terminal / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / Transcription Regulator spoIIAA / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. ...Transcription Regulator spoIIAA - #130 / Jelly Rolls - #1000 / Fibrillar collagen, C-terminal / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / Transcription Regulator spoIIAA / 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) / Jelly Rolls / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Collagen alpha-1(III) chain
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.21 Å
AuthorsBourhis, J.M. / Mariano, N. / Zhao, Y. / Harlos, K. / Jones, E.Y. / Moali, C. / Aghajari, N. / Hulmes, D.J.S.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Structural Basis of Fibrillar Collagen Trimerization and Related Genetic Disorders.
Authors: Bourhis, J.M. / Mariano, N. / Zhao, Y. / Harlos, K. / Exposito, J. / Jones, E.Y. / Moali, C. / Aghajari, N. / Hulmes, D.J.S.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Production and Crystallization of the C-Propeptide Trimer from Human Procollagen III.
Authors: Bourhis, J. / Mariano, N. / Zhao, Y. / Walter, T.S. / El Omari, K. / Delolme, F. / Moali, C. / Hulmes, D.J.S. / Aghajari, N.
History
DepositionJan 11, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references / Other
Revision 1.2Apr 3, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval ..._entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,05513
Polymers87,2903
Non-polymers76510
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-68.7 kcal/mol
Surface area27990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.930, 89.270, 101.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein COLLAGEN ALPHA-1(III) CHAIN / PROCOLLAGEN III


Mass: 29096.707 Da / Num. of mol.: 3
Fragment: CPROPEPTIDE OF PROCOLLAGEN III, RESIDUES 1222-1466
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: P02461
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN1064 TO GLN ENGINEERED RESIDUE IN CHAIN B, ASN1064 TO GLN ...ENGINEERED RESIDUE IN CHAIN A, ASN1064 TO GLN ENGINEERED RESIDUE IN CHAIN B, ASN1064 TO GLN ENGINEERED RESIDUE IN CHAIN C, ASN1064 TO GLN

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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: 2.3 Å3/Da / Density % sol: 46.5 % / Description: NONE
Crystal growDetails: 20% PEG 3350, 0.2 M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9796
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.2→101.5 Å / Num. obs: 38676 / % possible obs: 100 % / Observed criterion σ(I): 4 / Redundancy: 14.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 19
Reflection shellResolution: 2.21→2.27 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.21→39.41 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.65 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23686 1932 5 %RANDOM
Rwork0.20125 ---
obs0.20308 36672 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.634 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.21→39.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5028 0 45 179 5252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.025214
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3121.9597055
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3915639
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.99124.298242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.18815804
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8871527
X-RAY DIFFRACTIONr_chiral_restr0.0860.2735
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214011
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.215→2.272 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 112 -
Rwork0.245 2493 -
obs--100 %

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