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- PDB-8tys: Adaptive mechanism of collagen IV scaffold assembly in Drosophila... -

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Basic information

Entry
Database: PDB / ID: 8tys
TitleAdaptive mechanism of collagen IV scaffold assembly in Drosophila: crystal structure of tissue-extracted NC1 hexamer
Components
  • Collagen IV, chain Viking
  • Collagen alpha-1(IV) chain
KeywordsSTRUCTURAL PROTEIN / collagen IV / trimerization domain / hexamer assembly / basement membrane
Function / homology
Function and homology information


oviduct morphogenesis / post-embryonic digestive tract morphogenesis / Collagen degradation / Collagen biosynthesis and modifying enzymes / Assembly of collagen fibrils and other multimeric structures / Collagen chain trimerization / anterior Malpighian tubule development / Malpighian tubule morphogenesis / somatic muscle development / dorsal closure ...oviduct morphogenesis / post-embryonic digestive tract morphogenesis / Collagen degradation / Collagen biosynthesis and modifying enzymes / Assembly of collagen fibrils and other multimeric structures / Collagen chain trimerization / anterior Malpighian tubule development / Malpighian tubule morphogenesis / somatic muscle development / dorsal closure / collagen type IV trimer / intestinal epithelial structure maintenance / basement membrane organization / extracellular matrix structural constituent conferring tensile strength / cardiac muscle cell development / extracellular matrix structural constituent / basement membrane / extracellular matrix organization / collagen-containing extracellular matrix / extracellular space / membrane
Similarity search - Function
Collagen IV, non-collagenous / Collagen IV, non-collagenous domain superfamily / C-terminal tandem repeated domain in type 4 procollagen / Collagen IV carboxyl-terminal non-collagenous (NC1) domain profile. / C-terminal tandem repeated domain in type 4 procollagens / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / C-type lectin fold
Similarity search - Domain/homology
Collagen alpha-1(IV) chain / Viking, isoform A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBoudko, S.P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK018381 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK131101 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Collagen IV of basement membranes: IV. Adaptive mechanism of collagen IV scaffold assembly in Drosophila.
Authors: Summers, J.A. / Yarbrough, M. / Liu, M. / McDonald, W.H. / Hudson, B.G. / Pastor-Pareja, J.C. / Boudko, S.P.
History
DepositionAug 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)153,24012
Polymers153,0186
Non-polymers2226
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.209, 145.209, 106.491
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "D" and resid 5 through 227)
d_1ens_2(chain "B" and resid 3 through 227)
d_2ens_2chain "E"
d_1ens_3chain "C"
d_2ens_3(chain "F" and (resid 2 through 198 or (resid 199...

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1GLYGLYASNASNAA5 - 2276 - 228
d_2ens_1GLYGLYASNASNDD5 - 2276 - 228
d_1ens_2SERSERARGARGBB3 - 2274 - 228
d_2ens_2SERSERARGARGEE3 - 2274 - 228
d_1ens_3TYRTYRASNASNCC2 - 2273 - 228
d_2ens_3TYRTYRASNASNFF2 - 2273 - 228

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.721686076597, -0.304772463807, -0.621516654766), (-0.320045954685, -0.649222459316, 0.689986076099), (-0.613791327518, 0.696867235293, 0.370993615362)-80.8431852723, -2.88529224146, -34.8501071895
2given(-0.722850887983, -0.299964798378, -0.622501175481), (-0.322354081261, -0.65045035405, 0.687751541773), (-0.61120736255, 0.697807607189, 0.373483739022)-81.0578707814, -2.8292199228, -34.9380689823
3given(-0.722089210415, -0.310374771352, -0.618267477319), (-0.317346111497, -0.645519359228, 0.694691444009), (-0.614718323885, 0.697833976079, 0.367626337617)-80.7864031948, -2.60701323775, -34.9971705604

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Components

#1: Protein
Collagen alpha-1(IV) chain / Collagen IV / chain Cg25c


Mass: 25383.422 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P08120
#2: Protein Collagen IV, chain Viking


Mass: 25742.234 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VMV5
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.12 Å3/Da / Density % sol: 41.93 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 35% MPD, 0.1 M NaCl, 100mM HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.9→40.63 Å / Num. obs: 28410 / % possible obs: 100 % / Redundancy: 11.5 % / Biso Wilson estimate: 76.53 Å2 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.039 / Rrim(I) all: 0.093 / Net I/σ(I): 17.3
Reflection shellResolution: 2.9→3.08 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 4562 / Rpim(I) all: 0.2 / Rrim(I) all: 0.49

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
iMOSFLMdata reduction
pointlessdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→40.63 Å / SU ML: 0.4428 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.9722
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2773 1335 4.7 %
Rwork0.2411 27053 -
obs0.2428 28388 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.82 Å2
Refinement stepCycle: LAST / Resolution: 2.9→40.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10466 0 6 0 10472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001710732
X-RAY DIFFRACTIONf_angle_d0.521314597
X-RAY DIFFRACTIONf_chiral_restr0.04331571
X-RAY DIFFRACTIONf_plane_restr0.00361920
X-RAY DIFFRACTIONf_dihedral_angle_d12.14233853
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.694285570663
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.843089991331
ens_3d_2CCX-RAY DIFFRACTIONTorsion NCS0.875467307331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-30.36141400.33952682X-RAY DIFFRACTION100
3-3.120.34681420.32192672X-RAY DIFFRACTION100
3.12-3.270.35071480.32182677X-RAY DIFFRACTION100
3.27-3.440.35571190.29262722X-RAY DIFFRACTION100
3.44-3.650.30411310.27932680X-RAY DIFFRACTION99.96
3.65-3.940.32731170.27122721X-RAY DIFFRACTION100
3.94-4.330.28781150.24452720X-RAY DIFFRACTION100
4.33-4.960.24081520.21452691X-RAY DIFFRACTION100
4.96-6.240.25791260.21452732X-RAY DIFFRACTION100
6.24-40.630.22861450.18782756X-RAY DIFFRACTION99.83

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