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- PDB-6mpx: Twelve chloride ions induce formation and stabilize the NC1 hexam... -

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Basic information

Entry
Database: PDB / ID: 6mpx
TitleTwelve chloride ions induce formation and stabilize the NC1 hexamer of collagen IV assembled from transition state trimers
Componentsfusion protein of non-collagenous domains of collagen type IV
KeywordsSTRUCTURAL PROTEIN
Function / homology
Function and homology information


collagen type IV trimer / retinal blood vessel morphogenesis / Anchoring fibril formation / renal tubule morphogenesis / Crosslinking of collagen fibrils / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / platelet-derived growth factor binding / basement membrane organization / Extracellular matrix organization ...collagen type IV trimer / retinal blood vessel morphogenesis / Anchoring fibril formation / renal tubule morphogenesis / Crosslinking of collagen fibrils / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / platelet-derived growth factor binding / basement membrane organization / Extracellular matrix organization / Collagen biosynthesis and modifying enzymes / Laminin interactions / collagen-activated tyrosine kinase receptor signaling pathway / Signaling by PDGF / NCAM1 interactions / Scavenging by Class A Receptors / blood vessel morphogenesis / extracellular matrix structural constituent / Assembly of collagen fibrils and other multimeric structures / branching involved in blood vessel morphogenesis / neuromuscular junction development / endodermal cell differentiation / Collagen degradation / Non-integrin membrane-ECM interactions / basement membrane / ECM proteoglycans / Integrin cell surface interactions / cellular response to transforming growth factor beta stimulus / epithelial cell differentiation / extracellular matrix organization / negative regulation of angiogenesis / response to activity / cellular response to amino acid stimulus / brain development / collagen-containing extracellular matrix / angiogenesis / molecular adaptor activity / endoplasmic reticulum lumen / DNA-templated transcription / extracellular space / extracellular exosome / 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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Collagen alpha-1(IV) chain / Collagen alpha-2(IV) chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBauer, R. / Boudko, S.P. / Hudson, B.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)RDK18381-45 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)5T32DK007569-30 United States
CitationJournal: J.Biol.Chem. / Year: 2019
Title: A chloride ring is an ancient evolutionary innovation mediating the assembly of the collagen IV scaffold of basement membranes.
Authors: Pedchenko, V. / Bauer, R. / Pokidysheva, E.N. / Al-Shaer, A. / Forde, N.R. / Fidler, A.L. / Hudson, B.G. / Boudko, S.P.
History
DepositionOct 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 29, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: fusion protein of non-collagenous domains of collagen type IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,19822
Polymers76,3101
Non-polymers1,88821
Water7,927440
1
A: fusion protein of non-collagenous domains of collagen type IV
hetero molecules

A: fusion protein of non-collagenous domains of collagen type IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,39644
Polymers152,6192
Non-polymers3,77642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area17000 Å2
ΔGint-365 kcal/mol
Surface area39360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.160, 121.160, 106.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein fusion protein of non-collagenous domains of collagen type IV / / Collagen alpha-2(IV) chain / Collagen alpha-1(IV) chain


Mass: 76309.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COL4A1, COL4A2 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P02462, UniProt: P08572

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Non-polymers , 7 types, 461 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 2.55 Å3/Da / Density % sol: 51.75 % / Mosaicity: 0.63 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: .085 M HEPES (pH 7.5), 1.68 M ammonium sulfate, and 1.5% (w/v) PEG 400

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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: RAYONIX MX-300 / Detector: CCD / Date: Mar 16, 2018
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.9→85.673 Å / Num. all: 62515 / Num. obs: 62515 / % possible obs: 99.9 % / Redundancy: 8.9 % / Biso Wilson estimate: 28.9 Å2 / Rpim(I) all: 0.041 / Rrim(I) all: 0.129 / Rsym value: 0.122 / Net I/av σ(I): 3.6 / Net I/σ(I): 9.5 / Num. measured all: 558146
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.9-290.4431.790000.1540.470.443100
2-2.1290.3072.485610.1060.3250.307100
2.12-2.2790.2263.280240.0770.2390.226100
2.27-2.4590.1923.574990.0650.2030.192100
2.45-2.6990.1624.169390.0540.1710.162100
2.69-390.144.662800.0460.1470.14100
3-3.4790.134.855840.0430.1370.1399.9
3.47-4.258.90.115.747450.0360.1160.1199.8
4.25-6.018.80.0956.737310.0320.1010.09599.7
6.01-40.3878.10.0619.821520.0210.0650.06198.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.22data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LI1

1li1


Resolution: 1.9→39.893 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 16.77
RfactorNum. reflection% reflection
Rfree0.1767 3162 5.07 %
Rwork0.1478 --
obs0.1492 62346 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.23 Å2 / Biso mean: 35.159 Å2 / Biso min: 17.01 Å2
Refinement stepCycle: final / Resolution: 1.9→39.893 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5187 0 106 440 5733
Biso mean--49.92 41.76 -
Num. residues----673
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.92840.25741440.209925212665100
1.9284-1.95850.25261380.189825502688100
1.9585-1.99060.21831180.171325802698100
1.9906-2.02490.20561320.17225202652100
2.0249-2.06180.23421460.164625332679100
2.0618-2.10140.21741770.16624942671100
2.1014-2.14430.20991270.157125502677100
2.1443-2.19090.19961290.158925462675100
2.1909-2.24190.1931480.149325582706100
2.2419-2.29790.1751180.155725602678100
2.2979-2.36010.22121340.162525432677100
2.3601-2.42950.21021330.153725592692100
2.4295-2.50790.18351580.153625242682100
2.5079-2.59750.17741310.143126052736100
2.5975-2.70150.19261350.145125332668100
2.7015-2.82440.18371460.147125782724100
2.8244-2.97330.17111290.147625752704100
2.9733-3.15950.15421280.14425962724100
3.1595-3.40330.17581250.141526062731100
3.4033-3.74560.16921370.129326092746100
3.7456-4.28710.13751350.124226282763100
4.2871-5.39910.12791400.12782655279599
5.3991-39.90210.19461540.18022761291598
Refinement TLS params.Method: refined / Origin x: 20.6292 Å / Origin y: 24.2647 Å / Origin z: 17.6963 Å
111213212223313233
T0.2685 Å2-0.016 Å20.0037 Å2-0.3011 Å2-0.0011 Å2--0.1846 Å2
L0.9891 °2-0.0738 °20.0334 °2-1.2002 °2-0.0358 °2--0.5587 °2
S-0.0143 Å °-0.3134 Å °0.0107 Å °0.2452 Å °0.0369 Å °0.0397 Å °0.0088 Å °-0.0699 Å °-0.0181 Å °
Refinement TLS groupSelection details: (chain A and resseq 4:676)

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