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- PDB-4ae2: Crystal structure of Human fibrillar procollagen type III C- prop... -

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Basic information

Entry
Database: PDB / ID: 4ae2
TitleCrystal structure of Human fibrillar procollagen type III C- propeptide trimer
ComponentsCOLLAGEN ALPHA-1(III) CHAIN
KeywordsSTRUCTURAL PROTEIN / FIBRILLAR COLLAGEN / EXTRACELLULAR MATRIX / FIBROSIS
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 / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / negative regulation of neuron migration / endochondral bone morphogenesis / platelet-derived growth factor binding ...collagen type III trimer / aorta smooth muscle tissue morphogenesis / limb joint morphogenesis / transforming growth factor beta1 production / elastic fiber assembly / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / negative regulation of neuron migration / endochondral bone morphogenesis / platelet-derived growth factor binding / Extracellular matrix organization / negative regulation of immune response / layer formation in cerebral cortex / basement membrane organization / Collagen biosynthesis and modifying enzymes / peptide cross-linking / Signaling by PDGF / tissue homeostasis / response to angiotensin / NCAM1 interactions / collagen fibril organization / digestive tract development / Assembly of collagen fibrils and other multimeric structures / extracellular matrix structural constituent / MET activates PTK2 signaling / Scavenging by Class A Receptors / skin development / Syndecan interactions / positive regulation of Rho protein signal transduction / SMAD binding / Collagen degradation / Non-integrin membrane-ECM interactions / ECM proteoglycans / chondrocyte differentiation / Integrin cell surface interactions / supramolecular fiber organization / response to cytokine / transforming growth factor beta receptor signaling pathway / cell-matrix adhesion / integrin-mediated signaling pathway / cellular response to amino acid stimulus / lung development / wound healing / response to radiation / cerebral cortex development / platelet activation / multicellular organism growth / neuron migration / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / heart development / protease binding / fibroblast proliferation / : / in utero embryonic development / 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. ...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
NITRATE ION / Collagen alpha-1(III) chain
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsBourhis, J.M. / Mariano, N. / Zhao, Y. / Harlos, K. / Jones, E.Y. / Moali, C. / Aghajari, N. / Hulmes, D.J.
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.Y. / Jones, E.Y. / Moali, C. / Aghajari, N. / Hulmes, D.J.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Production and Crystallization of the C-Propeptide Trimer from Human Procollagen III.
Authors: Bourhis, J.M. / Mariano, N. / Zhao, Y. / Walter, T.S. / El Omari, K. / Delolme, F. / Moali, C. / Hulmes, D.J. / Aghajari, N.
History
DepositionJan 5, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references / Structure summary
Revision 1.2Oct 31, 2012Group: Database references
Revision 1.3Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.4Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,87611
Polymers86,4463
Non-polymers4308
Water7,170398
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-55.5 kcal/mol
Surface area27710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.450, 90.360, 102.440
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: 28815.340 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-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O
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: 39.9 % / Description: NONE
Crystal growpH: 6.5
Details: 20% PEG 3350, 0.1 M BIS TRIS PROPANE PH 6.5, POTASSIUM NITRATE 0.2 M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: May 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.7→61.2 Å / Num. obs: 78019 / % possible obs: 96.6 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.6
Reflection shellResolution: 1.7→61 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→61.27 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.44 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21354 3914 5 %RANDOM
Rwork0.16102 ---
obs0.16376 74058 96.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.855 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2---0.09 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.68→61.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4991 0 23 398 5412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.025184
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2441.9457023
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0545640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.4624.357241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.81815842
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3621526
X-RAY DIFFRACTIONr_chiral_restr0.0840.2725
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214025
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_restr3.1335184
X-RAY DIFFRACTIONr_sphericity_free24.2175133
X-RAY DIFFRACTIONr_sphericity_bonded14.80355320
LS refinement shellResolution: 1.683→1.727 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 269 -
Rwork0.207 5115 -
obs--95.63 %

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