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- PDB-5nb0: Crystal structures of homooligomers of collagen type IV. alpha3NC1 -

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Basic information

Entry
Database: PDB / ID: 5nb0
TitleCrystal structures of homooligomers of collagen type IV. alpha3NC1
ComponentsCollagen alpha-3(IV) chain
KeywordsSTRUCTURAL PROTEIN / Non-collagenous domain of collagen type IV. A principal structural component of basement membranes
Function / homology
Function and homology information


collagen type IV trimer / Anchoring fibril formation / Crosslinking of collagen fibrils / glomerular basement membrane development / Collagen chain trimerization / metalloendopeptidase inhibitor activity / extracellular matrix structural constituent conferring tensile strength / 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 / metalloendopeptidase inhibitor activity / extracellular matrix structural constituent conferring tensile strength / Extracellular matrix organization / Collagen biosynthesis and modifying enzymes / collagen-activated tyrosine kinase receptor signaling pathway / Laminin interactions / Signaling by PDGF / endothelial cell apoptotic process / NCAM1 interactions / blood circulation / negative regulation of vascular endothelial cell proliferation / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / Non-integrin membrane-ECM interactions / basement membrane / ECM proteoglycans / Integrin cell surface interactions / response to glucose / extracellular matrix organization / negative regulation of angiogenesis / sensory perception of sound / : / integrin binding / collagen-containing extracellular matrix / 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
Noncollagenous (NC1) domain of collagen IV / Collagen IV, non-collagenous / 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) ...Noncollagenous (NC1) domain of collagen IV / Collagen IV, non-collagenous / 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 / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Collagen alpha-3(IV) chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsCasino, P. / Marina, A.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2013-42619-P Spain
Spanish Ministry of Economy and CompetitivenessBFU2016-78606-P Spain
CitationJournal: IUCrJ / Year: 2018
Title: Structures of collagen IV globular domains: insight into associated pathologies, folding and network assembly.
Authors: Casino, P. / Gozalbo-Rovira, R. / Rodriguez-Diaz, J. / Banerjee, S. / Boutaud, A. / Rubio, V. / Hudson, B.G. / Saus, J. / Cervera, J. / Marina, A.
History
DepositionFeb 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Oct 9, 2019Group: Data collection / Category: reflns_shell
Revision 1.4Jan 17, 2024Group: 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 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
B: Collagen alpha-3(IV) chain
C: Collagen alpha-3(IV) chain
D: Collagen alpha-3(IV) chain
E: Collagen alpha-3(IV) chain
F: Collagen alpha-3(IV) chain
G: Collagen alpha-3(IV) chain
H: Collagen alpha-3(IV) chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,10524
Polymers204,5388
Non-polymers56716
Water4,179232
1
A: Collagen alpha-3(IV) chain
B: Collagen alpha-3(IV) chain
C: Collagen alpha-3(IV) chain
D: Collagen alpha-3(IV) chain
E: Collagen alpha-3(IV) chain
F: Collagen alpha-3(IV) chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,82918
Polymers153,4036
Non-polymers42512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37680 Å2
ΔGint-353 kcal/mol
Surface area38770 Å2
MethodPISA
2
G: Collagen alpha-3(IV) chain
H: Collagen alpha-3(IV) chain
hetero molecules

G: Collagen alpha-3(IV) chain
H: Collagen alpha-3(IV) chain
hetero molecules

G: Collagen alpha-3(IV) chain
H: Collagen alpha-3(IV) chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,82918
Polymers153,4036
Non-polymers42512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area37340 Å2
ΔGint-356 kcal/mol
Surface area38780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.518, 131.518, 248.855
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11E-431-

HOH

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Components

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


Mass: 25567.246 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COL4A3 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q01955
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
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: 2.07 Å3/Da / Density % sol: 40.61 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 6% PEG3350, BisTrisPropane pH 7.5 and MgCl2 0.2 M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.503
11K, H, -L20.497
ReflectionResolution: 2.7→51.783 Å / Num. all: 43361 / Num. obs: 43361 / % possible obs: 98.4 % / Redundancy: 2.2 % / Rpim(I) all: 0.069 / Rrim(I) all: 0.11 / Rsym value: 0.084 / Net I/av σ(I): 6.9 / Net I/σ(I): 11.2 / Num. measured all: 96546
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
2.7-2.852.10.2642.10.2230.3470.26495
2.85-3.022.10.2022.90.1670.2630.20298.3
3.02-3.232.20.15340.1260.1990.15399.6
3.23-3.492.30.1075.90.0880.1390.10799.7
3.49-3.822.30.0847.50.070.110.08499.5
3.82-4.272.20.058110.0480.0760.05899
4.27-4.932.10.04114.80.0330.0530.04198.2
4.93-6.042.50.03815.80.0290.0480.03899.5
6.04-8.542.50.03417.30.0270.0440.03499.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
PHASERphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T60

1t60


Resolution: 2.7→51.78 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.321 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.06
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1758 2182 5 %RANDOM
Rwork0.1633 ---
obs0.1639 41166 98.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 56 Å2 / Biso mean: 26.648 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--5.37 Å2-0 Å2-0 Å2
2---5.37 Å2-0 Å2
3---10.74 Å2
Refinement stepCycle: final / Resolution: 2.7→51.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13886 0 16 232 14134
Biso mean--27.05 31.27 -
Num. residues----1804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01914356
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.94419548
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.56351798
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.30222.66594
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.912152164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.081590
X-RAY DIFFRACTIONr_chiral_restr0.0810.22080
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02111078
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 146 -
Rwork0.219 2894 -
all-3040 -
obs--93.68 %

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