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

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Basic information

Entry
Database: PDB / ID: 8txn
TitleAdaptive mechanism of collagen IV scaffold assembly in Drosophila: crystal structure of recombinant NC1 hexamer
ComponentsCollagen alpha-1(IV) chain, 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


post-embryonic digestive tract morphogenesis / Collagen degradation / Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / anterior Malpighian tubule development / Malpighian tubule morphogenesis / collagen type IV trimer / Integrin cell surface interactions / dorsal closure / somatic muscle development ...post-embryonic digestive tract morphogenesis / Collagen degradation / Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / anterior Malpighian tubule development / Malpighian tubule morphogenesis / collagen type IV trimer / Integrin cell surface interactions / dorsal closure / somatic muscle development / extracellular matrix structural constituent conferring tensile strength / basement membrane organization / intestinal epithelial structure maintenance / cardiac muscle cell development / extracellular matrix structural constituent / basement membrane / extracellular matrix / : / extracellular space
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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / Collagen alpha-1(IV) chain / Viking, isoform A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 23, 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
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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, Collagen IV - chain Viking, Collagen alpha-1(IV) chain
D: Collagen alpha-1(IV) chain, Collagen IV - chain Viking, Collagen alpha-1(IV) chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,85625
Polymers159,3882
Non-polymers2,46823
Water15,529862
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14460 Å2
ΔGint-32 kcal/mol
Surface area39860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.120, 139.120, 103.381
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

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein Collagen alpha-1(IV) chain, Collagen IV - chain Viking, Collagen alpha-1(IV) chain


Mass: 79694.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: residues 1550-1779 of the alpha-1(IV) chain, follwed by residues 1510-1739 of the Viking chain, followed by residues 1550-1779 of the alpha-1(IV) chain
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: Col4a1, Cg25C, DCg1, CG4145, vkg, 1209, 6072, alpha(IV)2/vkg, col4a2, ColIV, colIV, ColIValpha2, Coll IV, Coll IValpha2, coll-IV, coll. IV, collagen-IV, CT25584, DmColA2, Dmel\CG16858, l(2) ...Gene: Col4a1, Cg25C, DCg1, CG4145, vkg, 1209, 6072, alpha(IV)2/vkg, col4a2, ColIV, colIV, ColIValpha2, Coll IV, Coll IValpha2, coll-IV, coll. IV, collagen-IV, CT25584, DmColA2, Dmel\CG16858, l(2)01209, veg, Vkg, VkgC, CG16858, Dmel_CG16858, Col4a1
Plasmid: pcDNA-CVC / Cell line (production host): expiCHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P08120, UniProt: Q9VMV5

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Non-polymers , 9 types, 885 molecules

#2: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#9: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 862 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 1.93 Å3/Da / Density % sol: 36.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Na/K phosphate, 0.2 M sodium chloride, and 26 % (w/v) PEG 1,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.979 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: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.75→52.05 Å / Num. obs: 114327 / % possible obs: 100 % / Redundancy: 11.4 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.092 / Net I/σ(I): 17.7
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 11 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 5634 / Rrim(I) all: 0.589 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOSFLMdata reduction
Aimlessdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→51.69 Å / SU ML: 0.1357 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.46
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1644 2003 1.75 %
Rwork0.1416 112286 -
obs0.142 114289 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.37 Å2
Refinement stepCycle: LAST / Resolution: 1.75→51.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10422 0 156 862 11440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006210983
X-RAY DIFFRACTIONf_angle_d0.889114932
X-RAY DIFFRACTIONf_chiral_restr0.05891611
X-RAY DIFFRACTIONf_plane_restr0.00711952
X-RAY DIFFRACTIONf_dihedral_angle_d14.53844015
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.20851400.17067960X-RAY DIFFRACTION99.98
1.79-1.840.20921440.15857999X-RAY DIFFRACTION100
1.84-1.90.18261410.15997986X-RAY DIFFRACTION100
1.9-1.960.15961430.14658014X-RAY DIFFRACTION100
1.96-2.030.17771420.14797984X-RAY DIFFRACTION99.99
2.03-2.110.19031400.13888013X-RAY DIFFRACTION99.99
2.11-2.20.17321430.13938024X-RAY DIFFRACTION100
2.2-2.320.1631400.13657972X-RAY DIFFRACTION100
2.32-2.470.19471440.14928042X-RAY DIFFRACTION100
2.47-2.660.1731430.14228002X-RAY DIFFRACTION100
2.66-2.920.16341460.15638013X-RAY DIFFRACTION100
2.92-3.350.16721410.13318049X-RAY DIFFRACTION100
3.35-4.220.13631470.12728084X-RAY DIFFRACTION100
4.22-51.690.14871490.13998144X-RAY DIFFRACTION99.92
Refinement TLS params.Method: refined / Origin x: -46.1722433371 Å / Origin y: 5.28789600051 Å / Origin z: -0.777609654235 Å
111213212223313233
T0.10706891836 Å20.00897486720804 Å20.0129949057213 Å2-0.104799767551 Å2-0.00508448094123 Å2--0.079049906889 Å2
L0.840878557977 °20.107065483229 °2-0.0898773693449 °2-0.60339933281 °20.0909456199861 °2--0.445673606311 °2
S0.011498750632 Å °0.0224557629291 Å °-0.0863976732348 Å °-0.0117558460827 Å °-0.0148534977454 Å °-0.0137850761625 Å °-0.0132959239968 Å °-0.0205491662797 Å °0.00178667772278 Å °
Refinement TLS groupSelection details: all

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