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- PDB-5nb2: Crystal structures of homooligomers of collagen type IV. alpha2NC1 -

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Basic information

Entry
Database: PDB / ID: 5nb2
TitleCrystal structures of homooligomers of collagen type IV. alpha2NC1
ComponentsCollagen 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 / Crosslinking of collagen fibrils / glomerular basement membrane development / Collagen chain trimerization / Extracellular matrix organization / extracellular matrix structural constituent conferring tensile strength / Collagen biosynthesis and modifying enzymes / Laminin interactions / 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 / Extracellular matrix organization / extracellular matrix structural constituent conferring tensile strength / Collagen biosynthesis and modifying enzymes / Laminin interactions / collagen-activated tyrosine kinase receptor signaling pathway / Signaling by PDGF / NCAM1 interactions / Scavenging by Class A Receptors / Assembly of collagen fibrils and other multimeric structures / extracellular matrix structural constituent / endodermal cell differentiation / Collagen degradation / Non-integrin membrane-ECM interactions / basement membrane / ECM proteoglycans / Integrin cell surface interactions / cellular response to transforming growth factor beta stimulus / negative regulation of angiogenesis / extracellular matrix organization / response to activity / angiogenesis / collagen-containing extracellular matrix / 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) / 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-2(IV) chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 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 1.3Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
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

Downloads & links

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Assembly

Deposited unit
A: Collagen alpha-2(IV) chain
B: Collagen alpha-2(IV) chain


Theoretical massNumber of molelcules
Total (without water)50,2292
Polymers50,2292
Non-polymers00
Water99155
1
A: Collagen alpha-2(IV) chain

A: Collagen alpha-2(IV) chain

A: Collagen alpha-2(IV) chain

A: Collagen alpha-2(IV) chain


Theoretical massNumber of molelcules
Total (without water)100,4584
Polymers100,4584
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area8880 Å2
ΔGint-71 kcal/mol
Surface area31700 Å2
MethodPISA
2
B: Collagen alpha-2(IV) chain

B: Collagen alpha-2(IV) chain

B: Collagen alpha-2(IV) chain

B: Collagen alpha-2(IV) chain


Theoretical massNumber of molelcules
Total (without water)100,4584
Polymers100,4584
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-y-1,x,z1
crystal symmetry operation4_545y,-x-1,z1
Buried area5500 Å2
ΔGint-39 kcal/mol
Surface area30090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.330, 94.330, 225.618
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A5 - 37
2116B5 - 37
1126A45 - 60
2126B45 - 60
1136A80 - 140
2136B80 - 140
1146A160 - 185
2146B160 - 185
1156A215 - 227
2156B215 - 227

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: Protein Collagen alpha-2(IV) chain


Mass: 25114.551 Da / Num. of mol.: 2
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 3.21 Å3/Da / Density % sol: 61.62 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 22% polyvinylpyrrolidone K15, 0.1M Na2SO4 and Mes pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→112.809 Å / Num. all: 18124 / Num. obs: 18124 / % possible obs: 100 % / Redundancy: 25.2 % / Rpim(I) all: 0.027 / Rrim(I) all: 0.137 / Rsym value: 0.134 / Net I/av σ(I): 4.5 / Net I/σ(I): 24.1 / Num. measured all: 456608
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
2.5-2.6426.41.6880.56835025930.3331.7211.6882.4100
2.64-2.825.61.170.76277924570.2341.1931.173.5100
2.8-2.9925.50.5941.35884623110.1190.6060.5947.3100
2.99-3.2325.80.3222.25590621630.0640.3280.32213.8100
3.23-3.5424.90.1963.34989920010.040.20.19621.9100
3.54-3.95250.1274.84562818230.0260.130.12732.4100
3.95-4.5624.90.07974022916150.0160.0810.07950.2100
4.56-5.5924.80.0668.23450613900.0130.0670.06656.3100
5.59-7.9123.70.0579.72615011040.0120.0580.05758.1100
7.91-112.80921.50.03713.6143156670.0080.0380.03772.699.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
SCALA3.3.21data scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LI1

1li1


Resolution: 2.5→112.81 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.904 / SU B: 22.318 / SU ML: 0.257 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.427 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2794 924 5.1 %RANDOM
Rwork0.2461 ---
obs0.2477 17196 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 120.09 Å2 / Biso mean: 62.084 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å2-0 Å20 Å2
2--0.3 Å2-0 Å2
3----0.61 Å2
Refinement stepCycle: final / Resolution: 2.5→112.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2739 0 0 55 2794
Biso mean---52.9 -
Num. residues----361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192826
X-RAY DIFFRACTIONr_bond_other_d0.0020.022539
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.9473852
X-RAY DIFFRACTIONr_angle_other_deg0.90235878
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4665351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65422.233103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.39415409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2371514
X-RAY DIFFRACTIONr_chiral_restr0.0720.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213102
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02604
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1506LOOSE POSITIONAL0.735
1506LOOSE THERMAL1.9210
2200LOOSE POSITIONAL0.65
2200LOOSE THERMAL3.5710
3824LOOSE POSITIONAL0.335
3824LOOSE THERMAL2.2110
4354LOOSE POSITIONAL0.485
4354LOOSE THERMAL5.2210
5208LOOSE POSITIONAL0.375
5208LOOSE THERMAL5.610
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 57 -
Rwork0.361 1260 -
all-1317 -
obs--99.85 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.35770.6599-0.4144.374-3.25066.32040.09650.5143-0.2228-0.45520.04280.12420.3985-0.0117-0.13930.18750.0398-0.00830.0503-0.02490.06230.596-22.3478-26.4726
28.1727-1.2183.19633.6752-0.11442.8050.0971-0.2871-0.11570.1573-0.012-0.0720.12970.0236-0.08510.23170.04750.02820.1642-0.00530.16878.3834-20.6434-16.4175
37.3574-2.3461.09662.5648-1.75534.64870.02770.0159-0.50590.04510.00540.10540.51790.1307-0.03310.246-0.04790.02440.0379-0.01440.0417-6.3046-23.2283-21.885
49.0545-5.35714.9914.3654-3.75153.9278-0.363-1.2022-0.28170.49530.3807-0.10150.0894-0.3076-0.01760.51210.00190.00290.33920.02870.1621-8.4421-22.5019-13.1003
56.54371.9499-2.72559.9042-3.80147.0835-0.0693-0.1305-0.6374-0.4549-0.38940.23510.70240.02450.45870.1386-0.06320.00380.1369-0.0140.1188-17.2234-19.8751-25.5867
64.8114-2.29063.3022.75451.39119.12910.51220.28690.1547-0.58140.1571-0.1149-0.6111.0219-0.66930.4178-0.32060.22290.4233-0.20750.3422-28.5645-34.9742-53.8827
72.59630.8909-1.47679.24297.379211.56260.4334-0.1937-0.01330.51620.2101-0.2698-0.49310.8543-0.64350.2956-0.20550.10640.3586-0.13690.1846-31.8159-31.9987-46.4205
81.01830.96441.5987.19052.92963.57710.09570.2859-0.0058-0.01230.4265-0.6288-0.21431.1207-0.52220.1841-0.21650.17790.7307-0.3370.2493-23.6458-41.3577-50.6497
90.170.20750.32119.70624.9942.85470.04250.272-0.01350.75180.0137-0.08060.37430.3856-0.05620.3181-0.10670.05460.6023-0.14450.3555-22.3893-40.7005-39.4434
1010.7892-0.85027.09173.0696-1.86055.84520.0042-0.035-0.00890.06710.0003-0.1397-0.06180.2864-0.00450.21220.08250.04260.3611-0.12810.2728-22.4235-51.0246-54.2233
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 37
2X-RAY DIFFRACTION2A46 - 64
3X-RAY DIFFRACTION3A75 - 140
4X-RAY DIFFRACTION4A155 - 195
5X-RAY DIFFRACTION5A214 - 227
6X-RAY DIFFRACTION6B7 - 37
7X-RAY DIFFRACTION7B46 - 60
8X-RAY DIFFRACTION8B80 - 140
9X-RAY DIFFRACTION9B160 - 194
10X-RAY DIFFRACTION10B213 - 228

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