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- PDB-6wku: Twelve Chloride Ions Drive Assembly of Human alpha345 Collagen IV... -

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Basic information

Entry
Database: PDB / ID: 6wku
TitleTwelve Chloride Ions Drive Assembly of Human alpha345 Collagen IV NC1 domain
ComponentsCollagen alpha-3(IV) chain,Collagen alpha-4(IV) chain,Collagen alpha-5(IV) chain
KeywordsSTRUCTURAL PROTEIN / collagen / chloride / hexamer / matrix
Function / homology
Function and homology information


collagen type IV trimer / Anchoring fibril formation / Crosslinking of collagen fibrils / glomerular basement membrane development / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / metalloendopeptidase inhibitor activity / Extracellular matrix organization / Collagen biosynthesis and modifying enzymes / collagen-activated tyrosine kinase receptor signaling pathway ...collagen type IV trimer / Anchoring fibril formation / Crosslinking of collagen fibrils / glomerular basement membrane development / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / metalloendopeptidase inhibitor activity / Extracellular matrix organization / Collagen biosynthesis and modifying enzymes / collagen-activated tyrosine kinase receptor signaling pathway / Signaling by PDGF / Laminin interactions / endothelial cell apoptotic process / NCAM1 interactions / negative regulation of vascular endothelial cell proliferation / extracellular matrix structural constituent / Assembly of collagen fibrils and other multimeric structures / neuromuscular junction development / Collagen degradation / basement membrane / Non-integrin membrane-ECM interactions / ECM proteoglycans / Integrin cell surface interactions / negative regulation of angiogenesis / neuromuscular junction / sensory perception of sound / integrin binding / Regulation of expression of SLITs and ROBOs / : / molecular adaptor activity / cell surface receptor signaling pathway / cell adhesion / endoplasmic reticulum lumen / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / structural molecule activity / endoplasmic reticulum / extracellular space / extracellular region
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
3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Collagen alpha-5(IV) chain / Collagen alpha-4(IV) chain / Collagen alpha-3(IV) chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsBoudko, S.P. / Hudson, B.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK018381 United States
Citation
Journal: J.Biol.Chem. / Year: 2021
Title: Collagen IV alpha 345 dysfunction in glomerular basement membrane diseases. II. Crystal structure of the alpha 345 hexamer.
Authors: Boudko, S.P. / Bauer, R. / Chetyrkin, S.V. / Ivanov, S. / Smith, J. / Voziyan, P.A. / Hudson, B.G.
#1: Journal: J.Biol.Chem. / Year: 2021
Title: Collagen IV alpha 345 dysfunction in glomerular basement membrane diseases. I. Discovery of a COL4A3 variant in familial Goodpasture's and Alport diseases.
Authors: Pokidysheva, E.N. / Seeger, H. / Pedchenko, V. / Chetyrkin, S. / Bergmann, C. / Abrahamson, D. / Cui, Z.W. / Delpire, E. / Fervenza, F. / Fidler, A.L. / Fogo, A.B. / Gaspert, A. / Grohmann, ...Authors: Pokidysheva, E.N. / Seeger, H. / Pedchenko, V. / Chetyrkin, S. / Bergmann, C. / Abrahamson, D. / Cui, Z.W. / Delpire, E. / Fervenza, F. / Fidler, A.L. / Fogo, A.B. / Gaspert, A. / Grohmann, M. / Gross, O. / Haddad, G. / Harris, R.C. / Kashtan, C. / Kitching, A.R. / Lorenzen, J.M. / McAdoo, S. / Pusey, C.D. / Segelmark, M. / Simmons, A. / Voziyan, P.A. / Wagner, T. / Wuthrich, R.P. / Zhao, M.H. / Boudko, S.P. / Kistler, A.D. / Hudson, B.G.
#2: Journal: J.Biol.Chem. / Year: 2021
Title: Collagen IV alpha 345 dysfunction in glomerular basement membrane diseases. III. A functional framework for alpha 345 hexamer assembly.
Authors: Pedchenko, V. / Boudko, S.P. / Barber, M. / Mikhailova, T. / Saus, J. / Harmange, J.C. / Hudson, B.G.
History
DepositionApr 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 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-3(IV) chain,Collagen alpha-4(IV) chain,Collagen alpha-5(IV) chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,16594
Polymers76,7071
Non-polymers10,45893
Water6,431357
1
A: Collagen alpha-3(IV) chain,Collagen alpha-4(IV) chain,Collagen alpha-5(IV) chain
hetero molecules

A: Collagen alpha-3(IV) chain,Collagen alpha-4(IV) chain,Collagen alpha-5(IV) chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,331188
Polymers153,4142
Non-polymers20,917186
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7480 Å2
ΔGint0 kcal/mol
Surface area41240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.420, 128.420, 104.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-489-

LYS

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Collagen alpha-3(IV) chain,Collagen alpha-4(IV) chain,Collagen alpha-5(IV) chain / Goodpasture antigen


Mass: 76707.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COL4A3, COL4A4, COL4A5 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
References: UniProt: Q01955, UniProt: P53420, UniProt: P29400

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Non-polymers , 9 types, 450 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical...
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#9: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.82 Å3/Da / Density % sol: 56.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 200, sodium chloride, tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Apr 14, 2018 / Details: MD2
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.76→68.6 Å / Num. obs: 86926 / % possible obs: 100 % / Redundancy: 8.2 % / Biso Wilson estimate: 20.597 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.031 / Rrim(I) all: 0.089 / Net I/σ(I): 13.1
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 4534 / CC1/2: 0.937 / Rpim(I) all: 0.182 / Rrim(I) all: 0.521 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMccp4_7.0data processing
MOLREP11.5.04phasing
PHENIX1.17.1_3660refinement
iMOSFLM7.2.0data reduction
Aimlessdata scaling
pointlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6mpx

6mpx


Resolution: 1.76→45.4 Å / SU ML: 0.1528 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.6046
RfactorNum. reflection% reflection
Rfree0.1615 2000 2.3 %
Rwork0.139 --
obs0.1395 86814 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 30.49 Å2
Refinement stepCycle: LAST / Resolution: 1.76→45.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5231 0 684 357 6272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00596165
X-RAY DIFFRACTIONf_angle_d0.89628132
X-RAY DIFFRACTIONf_chiral_restr0.057815
X-RAY DIFFRACTIONf_plane_restr0.00611005
X-RAY DIFFRACTIONf_dihedral_angle_d18.74082382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.80.23011410.19675993X-RAY DIFFRACTION100
1.8-1.850.1921410.17175973X-RAY DIFFRACTION99.98
1.85-1.910.20361410.15855976X-RAY DIFFRACTION99.97
1.91-1.970.17841410.14945993X-RAY DIFFRACTION100
1.97-2.040.18941420.14786008X-RAY DIFFRACTION99.98
2.04-2.120.18471410.14835970X-RAY DIFFRACTION99.98
2.12-2.220.1771420.14136033X-RAY DIFFRACTION99.95
2.22-2.330.17011420.13976031X-RAY DIFFRACTION99.98
2.33-2.480.14851420.14166011X-RAY DIFFRACTION99.98
2.48-2.670.15211430.13616064X-RAY DIFFRACTION99.95
2.67-2.940.16071430.13736044X-RAY DIFFRACTION99.97
2.94-3.370.14711440.12926129X-RAY DIFFRACTION99.98
3.37-4.240.13011450.12136171X-RAY DIFFRACTION100
4.24-45.40.16961520.14186418X-RAY DIFFRACTION99.7
Refinement TLS params.Method: refined / Origin x: -24.2767800901 Å / Origin y: -33.5038101238 Å / Origin z: 17.1091496979 Å
111213212223313233
T0.179969561454 Å20.00372069082167 Å2-0.00649090214641 Å2-0.157677238753 Å20.0189600667476 Å2--0.149159676705 Å2
L0.542518533776 °20.0190879954312 °20.0303539310633 °2-0.613713157544 °2-0.0432140574163 °2--0.47321450682 °2
S0.0120013620812 Å °-0.109335461285 Å °-0.050260007046 Å °0.138342029555 Å °-0.0026555418716 Å °0.00146195926516 Å °0.013502081702 Å °0.0176083569481 Å °-0.00931700573267 Å °
Refinement TLS groupSelection details: all

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