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- PDB-4ak3: Crystal structure of Human fibrillar procollagen type III C- prop... -

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Basic information

Entry
Database: PDB / ID: 4ak3
TitleCrystal structure of Human fibrillar procollagen type III C- propeptide trimer
ComponentsCOLLAGEN ALPHA-1(III) CHAIN
KeywordsSTRUCTURAL PROTEIN / FIBRILLAR COLLAGEN / EXTACELLULAR 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 / negative regulation of neuron migration / Collagen chain trimerization / platelet-derived growth factor binding / endochondral bone morphogenesis / basement membrane organization ...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 / basement membrane organization / Extracellular matrix organization / layer formation in cerebral cortex / extracellular matrix structural constituent conferring tensile strength / Collagen biosynthesis and modifying enzymes / peptide cross-linking / tissue homeostasis / Signaling by PDGF / negative regulation of immune response / digestive tract development / NCAM1 interactions / response to angiotensin / collagen fibril organization / Scavenging by Class A Receptors / skin development / Assembly of collagen fibrils and other multimeric structures / MET activates PTK2 signaling / extracellular matrix structural constituent / 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 / transforming growth factor beta receptor signaling pathway / cell-matrix adhesion / response to cytokine / integrin-mediated signaling pathway / cellular response to amino acid stimulus / lung development / neuron migration / wound healing / response to radiation / multicellular organism growth / platelet activation / cerebral cortex development / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / heart development / fibroblast proliferation / collagen-containing extracellular matrix / protease binding / in utero embryonic development / endoplasmic reticulum lumen / extracellular space / extracellular region / metal ion binding
Similarity search - Function
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 / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain ...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 / 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 / Mainly Beta
Similarity search - Domain/homology
Collagen alpha-1(III) chain
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 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.M. / Mariano, N. / Zhao, Y. / Walter, T.S. / El Omari, K. / Delolme, F. / Moali, C. / Hulmes, D.J. / Aghajari, N.
History
DepositionFeb 21, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
Revision 1.2Oct 31, 2012Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8552
Polymers28,8151
Non-polymers401
Water181
1
A: COLLAGEN ALPHA-1(III) CHAIN
hetero molecules

A: COLLAGEN ALPHA-1(III) CHAIN
hetero molecules

A: COLLAGEN ALPHA-1(III) CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5666
Polymers86,4463
Non-polymers1203
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation2_655-y+1,x-y,z1
Buried area3310 Å2
ΔGint-72.3 kcal/mol
Surface area30290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.047, 86.047, 72.952
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

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


Mass: 28815.340 Da / Num. of mol.: 1 / Fragment: CPROPEPTIDE, 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.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.83 Å3/Da / Density % sol: 56.5 % / Description: NONE

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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: 3.5→43.03 Å / Num. obs: 4149 / % possible obs: 99.7 % / Observed criterion σ(I): 3.2 / Redundancy: 7.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.7
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 3.2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0116refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AE2

4ae2


Resolution: 3.5→43.02 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.776 / SU B: 97.657 / SU ML: 0.716 / Cross valid method: THROUGHOUT / ESU R Free: 0.759 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.33715 192 4.6 %RANDOM
Rwork0.28276 ---
obs0.28538 3954 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.734 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 3.5→43.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1553 0 1 1 1555
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191619
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.9262222
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2915223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75924.03262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.77915179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.008156
X-RAY DIFFRACTIONr_chiral_restr0.0780.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211289
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: 3.501→3.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 8 -
Rwork0.357 257 -
obs--99.62 %
Refinement TLS params.Method: refined / Origin x: 24.133 Å / Origin y: 17.6626 Å / Origin z: 0.1744 Å
111213212223313233
T0.2483 Å20.0373 Å20.045 Å2-0.2227 Å2-0.0228 Å2--0.4328 Å2
L5.2604 °2-1.0753 °2-2.7492 °2-2.5658 °21.3016 °2--6.8709 °2
S-0.4975 Å °-0.1981 Å °-0.7822 Å °0.4534 Å °0.2466 Å °0.4391 Å °0.5723 Å °-0.2731 Å °0.2509 Å °

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