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- PDB-5nb1: Crystal structures of homooligomers of collagen type IV. alpha4NC1 -

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Basic information

Entry
Database: PDB / ID: 5nb1
TitleCrystal structures of homooligomers of collagen type IV. alpha4NC1
ComponentsCollagen alpha-4(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 / extracellular matrix structural constituent conferring tensile strength / Extracellular matrix organization / Collagen biosynthesis and modifying enzymes / Signaling by PDGF / Laminin interactions ...collagen type IV trimer / Anchoring fibril formation / Crosslinking of collagen fibrils / glomerular basement membrane development / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / Extracellular matrix organization / Collagen biosynthesis and modifying enzymes / Signaling by PDGF / Laminin interactions / NCAM1 interactions / extracellular matrix structural constituent / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / basement membrane / Non-integrin membrane-ECM interactions / ECM proteoglycans / Integrin cell surface interactions / : / molecular adaptor activity / 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-4(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, 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 6, 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-4(IV) chain
B: Collagen alpha-4(IV) chain
C: Collagen alpha-4(IV) chain
D: Collagen alpha-4(IV) chain
E: Collagen alpha-4(IV) chain
F: Collagen alpha-4(IV) chain


Theoretical massNumber of molelcules
Total (without water)152,6636
Polymers152,6636
Non-polymers00
Water1,20767
1
A: Collagen alpha-4(IV) chain
C: Collagen alpha-4(IV) chain
E: Collagen alpha-4(IV) chain

A: Collagen alpha-4(IV) chain
C: Collagen alpha-4(IV) chain
E: Collagen alpha-4(IV) chain

B: Collagen alpha-4(IV) chain
D: Collagen alpha-4(IV) chain
F: Collagen alpha-4(IV) chain

B: Collagen alpha-4(IV) chain
D: Collagen alpha-4(IV) chain
F: Collagen alpha-4(IV) chain


Theoretical massNumber of molelcules
Total (without water)305,32712
Polymers305,32712
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
crystal symmetry operation6_454-x-1/2,-y+1/2,z-1/21
crystal symmetry operation8_555x+1/2,-y+1/2,-z1
Buried area31270 Å2
ΔGint-179 kcal/mol
Surface area99330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.580, 167.561, 155.412
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Collagen alpha-4(IV) chain


Mass: 25443.912 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COL4A4 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P53420
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 3.45 Å3/Da / Density % sol: 64.37 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 6% PEG3350, 0.2 M sodium acetate and 0.1 M Mes pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98 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: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.82→47.464 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) obsRpim(I) allRrim(I) allRsym value% possible all
2.82-2.975.30.3672.10.1660.4050.36799.8
2.97-3.155.60.2323.20.0990.2540.23299.7
3.15-3.375.50.1684.40.0720.1850.16899.5
3.37-3.645.20.126.10.0530.1320.1299.2
3.64-3.995.60.097.80.0380.0980.0998.9
3.99-4.465.40.0778.80.0340.0850.07798.6
4.46-5.155.20.06610.10.0290.0730.06698.3
5.15-6.315.40.06410.30.0280.070.06498.1
6.31-8.925.10.059110.0260.0650.05996.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T60

1t60


Resolution: 2.82→47.46 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.915 / SU B: 14.396 / SU ML: 0.266 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.181 / ESU R Free: 0.079
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2807 2373 5.1 %RANDOM
Rwork0.2317 ---
obs0.2341 44524 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 147.78 Å2 / Biso mean: 56.903 Å2 / Biso min: 21.47 Å2
Baniso -1Baniso -2Baniso -3
1--36.99 Å20 Å20 Å2
2--5.31 Å20 Å2
3---31.68 Å2
Refinement stepCycle: final / Resolution: 2.82→47.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9548 0 0 67 9615
Biso mean---47.64 -
Num. residues----1247
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.029936
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.93713582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85751254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.98623.767438
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.114151445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1771549
X-RAY DIFFRACTIONr_chiral_restr0.0890.21437
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217761
LS refinement shellResolution: 2.798→2.871 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 180 -
Rwork0.324 3188 -
all-3368 -
obs--97.91 %

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