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- PDB-5naz: Crystal structures of homooligomers of collagen type IV. alpha5NC1 -

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Basic information

Entry
Database: PDB / ID: 5naz
TitleCrystal structures of homooligomers of collagen type IV. alpha5NC1
ComponentsCollagen alpha-5(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 / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / Extracellular matrix organization / Collagen biosynthesis and modifying enzymes / Laminin interactions / collagen-activated tyrosine kinase receptor signaling pathway / Signaling by PDGF ...collagen type IV trimer / Anchoring fibril formation / Crosslinking of collagen fibrils / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / Extracellular matrix organization / Collagen biosynthesis and modifying enzymes / Laminin interactions / collagen-activated tyrosine kinase receptor signaling pathway / Signaling by PDGF / NCAM1 interactions / extracellular matrix structural constituent / Assembly of collagen fibrils and other multimeric structures / neuromuscular junction development / Collagen degradation / Non-integrin membrane-ECM interactions / basement membrane / ECM proteoglycans / Integrin cell surface interactions / extracellular matrix organization / neuromuscular junction / Regulation of expression of SLITs and ROBOs / collagen-containing extracellular matrix / endoplasmic reticulum lumen / 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) / C-type lectin fold ...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-5(IV) chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 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 / citation_author
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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Collagen alpha-5(IV) chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8215
Polymers25,3621
Non-polymers4594
Water2,090116
1
A: Collagen alpha-5(IV) chain
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)154,92730
Polymers152,1716
Non-polymers2,75624
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544-z,x-1/2,-y-1/21
crystal symmetry operation11_545y+1/2,-z-1/2,-x1
crystal symmetry operation14_444-y-1/4,-x-1/4,-z-1/41
crystal symmetry operation18_545-x+1/4,z-1/4,y+1/41
crystal symmetry operation22_544z+1/4,-y-3/4,x-1/41
Buried area43880 Å2
ΔGint-283 kcal/mol
Surface area36920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.283, 121.283, 121.283
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-40-

LYS

21A-506-

HOH

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Components

#1: Protein Collagen alpha-5(IV) chain


Mass: 25361.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COL4A5 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P29400
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.96 Å3/Da / Density % sol: 58.46 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 20%PEG8000, 0.2 M NaCl, CAPS pH 10.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.85→42.88 Å / Num. all: 26393 / Num. obs: 26393 / % possible obs: 99.3 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.049 / Rrim(I) all: 0.112 / Rsym value: 0.1 / Net I/av σ(I): 6 / Net I/σ(I): 12.1 / Num. measured all: 125648
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
1.85-1.954.80.35420.1740.3960.35499.9
1.95-2.074.90.2522.70.1250.2830.25299.6
2.07-2.214.90.1714.30.0840.1910.17199
2.21-2.394.80.1374.40.0680.1540.13799
2.39-2.624.80.1086.80.0530.1210.10899.5
2.62-2.934.70.0887.50.0440.0990.088100
2.93-3.384.70.0846.90.0410.0940.084100
3.38-4.144.40.05910.10.030.0670.059100
4.14-5.854.60.04711.70.0230.0530.04796.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALA3.2.25data scaling
PHASERphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T60

1t60


Resolution: 1.85→42.87 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.148 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.099
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1904 1333 5.1 %RANDOM
Rwork0.1852 ---
obs0.1855 25014 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 39.49 Å2 / Biso mean: 13.508 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.85→42.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1752 0 25 116 1893
Biso mean--27.59 18.82 -
Num. residues----226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191841
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.942493
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9475229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.03823.29382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54815289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4921512
X-RAY DIFFRACTIONr_chiral_restr0.0910.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211410
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 89 -
Rwork0.25 1845 -
all-1934 -
obs--99.9 %

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