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- PDB-5nay: Crystal structures of homooligomers of collagen type IV. alpha1NC1 -

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Basic information

Entry
Database: PDB / ID: 5nay
TitleCrystal structures of homooligomers of collagen type IV. alpha1NC1
ComponentsCollagen alpha-1(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 / retinal blood vessel morphogenesis / Crosslinking of collagen fibrils / renal tubule morphogenesis / Collagen chain trimerization / platelet-derived growth factor binding / extracellular matrix structural constituent conferring tensile strength / Extracellular matrix organization / basement membrane organization ...collagen type IV trimer / Anchoring fibril formation / retinal blood vessel morphogenesis / Crosslinking of collagen fibrils / renal tubule morphogenesis / Collagen chain trimerization / platelet-derived growth factor binding / extracellular matrix structural constituent conferring tensile strength / Extracellular matrix organization / basement membrane organization / Collagen biosynthesis and modifying enzymes / collagen-activated tyrosine kinase receptor signaling pathway / Signaling by PDGF / Laminin interactions / NCAM1 interactions / blood vessel morphogenesis / extracellular matrix structural constituent / Assembly of collagen fibrils and other multimeric structures / Scavenging by Class A Receptors / branching involved in blood vessel morphogenesis / neuromuscular junction development / Collagen degradation / basement membrane / Non-integrin membrane-ECM interactions / ECM proteoglycans / Integrin cell surface interactions / epithelial cell differentiation / cellular response to amino acid stimulus / brain development / : / 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) ...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-1(IV) chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Collagen alpha-1(IV) chain
B: Collagen alpha-1(IV) chain
C: Collagen alpha-1(IV) chain
D: Collagen alpha-1(IV) chain
E: Collagen alpha-1(IV) chain
F: Collagen alpha-1(IV) chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,33526
Polymers152,1416
Non-polymers1,19420
Water14,214789
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41560 Å2
ΔGint-488 kcal/mol
Surface area38320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.851, 127.045, 130.543
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 25356.871 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COL4A1 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P02462
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 789 / 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: 2.59 Å3/Da / Density % sol: 52.45 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 1.4 M lithium sulfate and 0.1 M Mes pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.8→91.046 Å / Num. all: 142960 / Num. obs: 142960 / % possible obs: 98.2 % / Redundancy: 3.4 % / Rpim(I) all: 0.048 / Rrim(I) all: 0.09 / Rsym value: 0.076 / Net I/av σ(I): 7.8 / Net I/σ(I): 10.7 / Num. measured all: 479345
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
1.8-1.93.30.3881.90.2480.4630.38899
1.9-2.013.30.2532.80.1630.3020.25399.4
2.01-2.153.30.1763.70.1130.210.17699.3
2.15-2.323.30.1255.80.080.150.12599.2
2.32-2.553.40.0987.60.0620.1160.09898.9
2.55-2.853.40.0739.90.0460.0870.07398.4
2.85-3.293.40.05910.70.0370.070.05997.5
3.29-4.023.40.04812.30.030.0570.04896.5
4.02-5.693.50.03714.90.0230.0440.03794.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHASERphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T60

1t60


Resolution: 1.8→57.12 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.585 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.107
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1994 7122 5 %RANDOM
Rwork0.1755 ---
obs0.1767 135786 97.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 58.9 Å2 / Biso mean: 19.085 Å2 / Biso min: 9.82 Å2
Baniso -1Baniso -2Baniso -3
1-1.43 Å20 Å20 Å2
2---0.47 Å20 Å2
3----0.96 Å2
Refinement stepCycle: final / Resolution: 1.8→57.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10597 0 52 789 11438
Biso mean--28.96 26.72 -
Num. residues----1370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01910990
X-RAY DIFFRACTIONr_angle_refined_deg1.2731.94214962
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.02451372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.4422.58469
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.616151691
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9221578
X-RAY DIFFRACTIONr_chiral_restr0.0880.21580
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218476
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 483 -
Rwork0.268 10070 -
all-10553 -
obs--98.67 %

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