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- PDB-5nax: Crystal structures of homooligomers of the non-collagenous domain... -

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Basic information

Entry
Database: PDB / ID: 5nax
TitleCrystal structures of homooligomers of the non-collagenous domains of collagen type IV. alpha121NC1
Components
  • Collagen alpha-1(IV) chain
  • Collagen alpha-2(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 / endodermal cell differentiation / Collagen degradation / basement membrane / Non-integrin membrane-ECM interactions / ECM proteoglycans / Integrin cell surface interactions / cellular response to transforming growth factor beta stimulus / extracellular matrix organization / epithelial cell differentiation / negative regulation of angiogenesis / response to activity / cellular response to amino acid stimulus / brain development / : / angiogenesis / molecular adaptor activity / endoplasmic reticulum lumen / DNA-templated transcription / extracellular space / extracellular exosome / 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 / Collagen alpha-2(IV) chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.82 Å
AuthorsCasino, P. / Marina, A.
Funding support Spain, 3items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2013-42619-P Spain
Spanish Ministry of Economy and CompetitivenessBFU2016-78606-P Spain
European UnionFP7/2007-2013 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
Revision 1.3Jan 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 1.4Nov 20, 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-2(IV) chain
D: Collagen alpha-1(IV) chain
E: Collagen alpha-2(IV) chain
F: Collagen alpha-1(IV) chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,04717
Polymers151,6576
Non-polymers39011
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38600 Å2
ΔGint-326 kcal/mol
Surface area37880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.148, 126.148, 216.211
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 25356.871 Da / Num. of mol.: 4 / Fragment: UNP residues 1443-1667
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: Protein Collagen alpha-2(IV) chain


Mass: 25114.551 Da / Num. of mol.: 2 / Fragment: UNP residues 1485-1712
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COL4A2 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P08572
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 3.32 Å3/Da / Density % sol: 62.93 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 10% PEG8000, Magnesium acetate 0.2 M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.25 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.25 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.521
11-h,-k,l20.479
ReflectionResolution: 2.82→48.75 Å / Num. all: 48121 / Num. obs: 48121 / % possible obs: 98.9 % / Redundancy: 5.4 % / Rpim(I) all: 0.04 / Rrim(I) all: 0.101 / Rsym value: 0.092 / Net I/av σ(I): 7.1 / Net I/σ(I): 12.7 / Num. measured all: 258124
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.82-2.975.30.3672.13670969760.1660.4050.3673.699.8
2.97-3.155.60.2323.23755466590.0990.2540.2325.899.7
3.15-3.375.50.1684.43420061990.0720.1850.1687.999.5
3.37-3.645.20.126.13009457940.0530.1320.1211.199.2
3.64-3.995.60.097.82956053150.0380.0980.0915.398.9
3.99-4.465.40.0778.82589448370.0340.0850.07718.598.6
4.46-5.155.20.06610.12217342530.0290.0730.06621.398.3
5.15-6.315.40.06410.31955236450.0280.070.06420.998.1
6.31-8.925.10.059111441428100.0260.0650.05921.596.9
8.92-48.4474.90.05411.2797416330.0260.060.05423.495.8

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Phasing

PhasingMethod: molecular replacement

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Processing

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

1t60


Resolution: 2.82→48.45 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.152 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1848 2457 5.1 %RANDOM
Rwork0.1409 ---
obs0.1431 45615 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 147.79 Å2 / Biso mean: 65.262 Å2 / Biso min: 27.85 Å2
Baniso -1Baniso -2Baniso -3
1-30.05 Å20 Å20 Å2
2--30.05 Å20 Å2
3----60.1 Å2
Refinement stepCycle: final / Resolution: 2.82→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10391 0 11 141 10543
Biso mean--65.3 50.94 -
Num. residues----1348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01910724
X-RAY DIFFRACTIONr_angle_refined_deg1.1871.94214606
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.95751350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.46222.94449
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.936151632
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0691563
X-RAY DIFFRACTIONr_chiral_restr0.0750.21535
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218289
LS refinement shellResolution: 2.82→2.893 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 156 -
Rwork0.202 3342 -
all-3498 -
obs--99.6 %

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