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- PDB-5k31: Crystal structure of Human fibrillar procollagen type I C-propept... -

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Basic information

Entry
Database: PDB / ID: 5k31
TitleCrystal structure of Human fibrillar procollagen type I C-propeptide Homo-trimer
ComponentsCollagen alpha-1(I) chain
KeywordsSTRUCTURAL PROTEIN / FIBRILLAR COLLAGEN / EXTRACELLULAR MATRIX / FIBROSIS
Function / homology
Function and homology information


cellular response to fluoride / collagen type I trimer / tooth mineralization / cellular response to vitamin E / bone trabecula formation / Anchoring fibril formation / Crosslinking of collagen fibrils / collagen biosynthetic process / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength ...cellular response to fluoride / collagen type I trimer / tooth mineralization / cellular response to vitamin E / bone trabecula formation / Anchoring fibril formation / Crosslinking of collagen fibrils / collagen biosynthetic process / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / platelet-derived growth factor binding / intramembranous ossification / Extracellular matrix organization / embryonic skeletal system development / cartilage development involved in endochondral bone morphogenesis / Collagen biosynthesis and modifying enzymes / skin morphogenesis / collagen-activated tyrosine kinase receptor signaling pathway / Platelet Adhesion to exposed collagen / endochondral ossification / cellular response to fibroblast growth factor stimulus / collagen fibril organization / negative regulation of cell-substrate adhesion / face morphogenesis / response to steroid hormone / Scavenging by Class A Receptors / skin development / MET activates PTK2 signaling / Assembly of collagen fibrils and other multimeric structures / Syndecan interactions / GP1b-IX-V activation signalling / blood vessel development / RUNX2 regulates osteoblast differentiation / Platelet Aggregation (Plug Formation) / Collagen degradation / protein localization to nucleus / Non-integrin membrane-ECM interactions / ECM proteoglycans / response to hyperoxia / positive regulation of epithelial to mesenchymal transition / Integrin cell surface interactions / response to mechanical stimulus / cellular response to retinoic acid / response to cAMP / cellular response to epidermal growth factor stimulus / GPVI-mediated activation cascade / cellular response to transforming growth factor beta stimulus / visual perception / extracellular matrix organization / ossification / secretory granule / skeletal system development / cellular response to glucose stimulus / cellular response to amino acid stimulus / Cell surface interactions at the vascular wall / sensory perception of sound / response to insulin / response to hydrogen peroxide / osteoblast differentiation / cellular response to mechanical stimulus / positive regulation of canonical Wnt signaling pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / protein transport / response to estradiol / cellular response to tumor necrosis factor / collagen-containing extracellular matrix / protease binding / positive regulation of cell migration / response to xenobiotic stimulus / endoplasmic reticulum lumen / positive regulation of DNA-templated transcription / extracellular space / extracellular region / identical protein binding / metal ion binding / cytoplasm
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(I) chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSharma, U. / Hulmes, D.J.S. / Aghajari, N.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency2010-BLAN-1526-01 France
CitationJournal: Nat Commun / Year: 2017
Title: Structural basis of homo- and heterotrimerization of collagen I.
Authors: Sharma, U. / Carrique, L. / Vadon-Le Goff, S. / Mariano, N. / Georges, R.N. / Delolme, F. / Koivunen, P. / Myllyharju, J. / Moali, C. / Aghajari, N. / Hulmes, D.J.
History
DepositionMay 19, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Collagen alpha-1(I) chain
B: Collagen alpha-1(I) chain
C: Collagen alpha-1(I) chain
D: Collagen alpha-1(I) chain
E: Collagen alpha-1(I) chain
F: Collagen alpha-1(I) chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,93520
Polymers172,1286
Non-polymers80714
Water7,566420
1
D: Collagen alpha-1(I) chain
hetero molecules

A: Collagen alpha-1(I) chain
E: Collagen alpha-1(I) chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4049
Polymers86,0643
Non-polymers3406
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y+1/2,-z+21
2
A: Collagen alpha-1(I) chain
E: Collagen alpha-1(I) chain
hetero molecules

D: Collagen alpha-1(I) chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4049
Polymers86,0643
Non-polymers3406
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_647-x+1,y-1/2,-z+21
Buried area5880 Å2
ΔGint-83 kcal/mol
Surface area32300 Å2
MethodPISA
3
B: Collagen alpha-1(I) chain
C: Collagen alpha-1(I) chain
F: Collagen alpha-1(I) chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,53111
Polymers86,0643
Non-polymers4678
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-94 kcal/mol
Surface area32490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.820, 149.630, 105.950
Angle α, β, γ (deg.)90.00, 101.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Collagen alpha-1(I) chain / Alpha-1 type I collagen


Mass: 28687.947 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COL1A1 / Plasmid: PHLSEC / Cell (production host): HEK 293T / Production host: Homo sapiens (human) / References: UniProt: P02452
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / 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.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 3.37 Å3/Da / Density % sol: 63.55 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 18 % PEG 4000 and 0.1 M Tris pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→47.07 Å / Num. obs: 115206 / % possible obs: 99.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 7.7
Reflection shellHighest resolution: 2.2 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AEJ

2aej


Resolution: 2.2→47.07 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.923 / SU B: 11.206 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.173 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23811 5779 5 %RANDOM
Rwork0.19557 ---
obs0.19767 109357 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.469 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å21.06 Å2
2---1.06 Å2-0 Å2
3---0.4 Å2
Refinement stepCycle: 1 / Resolution: 2.2→47.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11088 0 39 420 11547
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01911381
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210283
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.94215460
X-RAY DIFFRACTIONr_angle_other_deg0.836323730
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.64551430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.84325.019526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.921151844
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6951553
X-RAY DIFFRACTIONr_chiral_restr0.0980.21686
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02113101
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022600
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_it1.9592.5685738
X-RAY DIFFRACTIONr_mcbond_other1.9592.5685737
X-RAY DIFFRACTIONr_mcangle_it2.9533.8417162
X-RAY DIFFRACTIONr_mcangle_other2.9523.8417163
X-RAY DIFFRACTIONr_scbond_it2.6522.8845643
X-RAY DIFFRACTIONr_scbond_other2.6522.8845644
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1444.1898299
X-RAY DIFFRACTIONr_long_range_B_refined5.76320.90812900
X-RAY DIFFRACTIONr_long_range_B_other5.76220.90812894
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 435 -
Rwork0.24 8017 -
obs--99.55 %
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)
10.28650.6055-0.05132.4741-0.58970.8472-0.0749-0.0285-0.02980.3561-0.0582-0.1424-0.1915-0.13140.13310.29060.0191-0.01420.0341-0.01460.025410.87735.0366111.433
20.43310.0715-0.7181.1377-0.57021.76330.03210.12-0.0445-0.0115-0.06620.0103-0.0879-0.19940.03410.12820.03730.0110.0515-0.00760.00887.890741.265770.066
31.2131-0.96470.85021.1265-0.77281.5062-0.1292-0.10130.1371-0.01490.1276-0.1542-0.22220.05350.00160.1949-0.00350.04210.042-0.02870.038440.737550.530663.4327
41.6548-0.9324-1.27110.7360.66332.7614-0.07920.0941-0.14730.00490.0340.046-0.0807-0.54380.04530.18290.03940.05450.15790.00090.0302-2.230956.9001108.4634
50.13260.2901-0.09681.2539-0.46692.79730.0335-0.01950.0155-0.0734-0.0890.0237-0.1661-0.23570.05550.15040.01420.03120.0357-0.0120.01316.5964-8.624979.7573
60.2377-0.5784-0.05522.4222-0.56251.0534-0.07230.0704-0.0062-0.1959-0.0546-0.1990.1087-0.16680.12690.2931-0.02630.10440.0466-0.02020.049724.597727.446942.6996
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 246
2X-RAY DIFFRACTION2B8 - 246
3X-RAY DIFFRACTION3C9 - 246
4X-RAY DIFFRACTION4D8 - 246
5X-RAY DIFFRACTION5E8 - 246
6X-RAY DIFFRACTION6F7 - 246

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