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- PDB-9i5b: Crystal structure of perlecan region 3 mutant (P1019L) construct ... -

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Basic information

Entry
Database: PDB / ID: 9i5b
TitleCrystal structure of perlecan region 3 mutant (P1019L) construct I876-V1272 including one laminin IV-like and four laminin EGF-like domains.
ComponentsBasement membrane-specific heparan sulfate proteoglycan core protein
KeywordsSTRUCTURAL PROTEIN / Basement membrane proteins / perlecan / laminin IV-like / laminin EGF-like domains
Function / homology
Function and homology information


embryonic skeletal system morphogenesis / cartilage development involved in endochondral bone morphogenesis / endochondral ossification / cardiac muscle tissue development / basement membrane / chondrocyte differentiation / extracellular matrix organization / extracellular matrix / receptor-mediated endocytosis / brain development ...embryonic skeletal system morphogenesis / cartilage development involved in endochondral bone morphogenesis / endochondral ossification / cardiac muscle tissue development / basement membrane / chondrocyte differentiation / extracellular matrix organization / extracellular matrix / receptor-mediated endocytosis / brain development / Golgi lumen / intracellular protein localization / protease binding / : / angiogenesis / calcium ion binding / extracellular region
Similarity search - Function
: / Laminin IV / Laminin B (Domain IV) / Laminin IV type A domain profile. / Laminin B domain / Laminin G domain / Laminin-type EGF-like (LE) domain profile. / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Domain found in sea urchin sperm protein, enterokinase, agrin ...: / Laminin IV / Laminin B (Domain IV) / Laminin IV type A domain profile. / Laminin B domain / Laminin G domain / Laminin-type EGF-like (LE) domain profile. / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Domain found in sea urchin sperm protein, enterokinase, agrin / Laminin EGF domain / Laminin-type EGF domain / SEA domain profile. / SEA domain / Laminin G domain profile. / Laminin G domain / Laminin G domain / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / EGF-like domain / Immunoglobulin domain / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Concanavalin A-like lectin/glucanase domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
SUCCINIC ACID / Basement membrane-specific heparan sulfate proteoglycan core protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsSohail, A.A. / Koski, M.K. / Ruddock, L.R.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland272573 Finland
CitationJournal: Matrix Biol. / Year: 2025
Title: Structural insights on perlecan and Schwartz-Jampel syndrome.
Authors: Sohail, A.A. / Koski, M.K. / Ruddock, L.W.
History
DepositionJan 27, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Basement membrane-specific heparan sulfate proteoglycan core protein
B: Basement membrane-specific heparan sulfate proteoglycan core protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,5824
Polymers85,3462
Non-polymers2362
Water4,179232
1
A: Basement membrane-specific heparan sulfate proteoglycan core protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7912
Polymers42,6731
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Basement membrane-specific heparan sulfate proteoglycan core protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7912
Polymers42,6731
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.65, 74.968, 81.368
Angle α, β, γ (deg.)75.235, 73.124, 80.112
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: CYS / End label comp-ID: CYS / Auth seq-ID: 876 - 1156 / Label seq-ID: 1 - 281

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Basement membrane-specific heparan sulfate proteoglycan core protein / HSPG


Mass: 42672.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Single point mutation at P1019L / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hspg2 / Production host: Escherichia coli B (bacteria) / References: UniProt: Q05793
#2: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.79 Å3/Da / Density % sol: 67.56 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.85M succinic acid, pH 7 / PH range: 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.7293 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7293 Å / Relative weight: 1
ReflectionResolution: 2.52→47.67 Å / Num. obs: 41874 / % possible obs: 98.5 % / Redundancy: 3.6 % / CC1/2: 0.994 / Net I/σ(I): 9.9
Reflection shellResolution: 2.52→2.58 Å / Num. unique obs: 3056 / CC1/2: 0.645

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.88)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.52→47.67 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / SU B: 19.223 / SU ML: 0.19 / Cross valid method: FREE R-VALUE / ESU R: 0.261 / ESU R Free: 0.208 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2202 1993 4.777 %
Rwork0.1883 39729 -
all0.19 --
obs-41722 98.545 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 58.623 Å2
Baniso -1Baniso -2Baniso -3
1--3.371 Å21.5 Å20.306 Å2
2---1.314 Å2-2.903 Å2
3---3.458 Å2
Refinement stepCycle: LAST / Resolution: 2.52→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5063 0 16 232 5311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125247
X-RAY DIFFRACTIONr_angle_refined_deg1.871.8057145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.825680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.725541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.38610788
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.25810247
X-RAY DIFFRACTIONr_chiral_restr0.1270.2741
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024169
X-RAY DIFFRACTIONr_nbd_refined0.2290.22255
X-RAY DIFFRACTIONr_nbtor_refined0.310.23575
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2359
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2510.264
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1630.29
X-RAY DIFFRACTIONr_mcbond_it3.0733.312702
X-RAY DIFFRACTIONr_mcangle_it4.8885.9443376
X-RAY DIFFRACTIONr_scbond_it4.5783.6092545
X-RAY DIFFRACTIONr_scangle_it7.0356.4643765
X-RAY DIFFRACTIONr_lrange_it10.0737.9787731
X-RAY DIFFRACTIONr_ncsr_local_group_10.0890.058459
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.088620.05009
12BX-RAY DIFFRACTIONLocal ncs0.088620.05009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.52-2.5850.3341460.33429210.33431120.9220.91698.5540.306
2.585-2.6560.2771410.32528190.32330180.9420.92398.07820.292
2.656-2.7330.3631410.31527940.31729950.8990.9297.99670.278
2.733-2.8160.3331350.27826980.28128690.9280.94698.74520.241
2.816-2.9080.3261310.25926160.26227830.9260.95598.70640.223
2.908-3.010.2721290.22525700.22727300.9470.96698.86450.194
3.01-3.1230.2711220.21424320.21725800.9550.9798.99220.185
3.123-3.250.2231190.19623780.19725210.9660.97699.0480.172
3.25-3.3940.2081150.1922820.19124140.9720.97999.29580.171
3.394-3.5590.2021070.17221470.17322830.9750.98398.72970.156
3.559-3.750.1771040.15520500.15621810.9790.98698.7620.143
3.75-3.9760.196960.15319160.15520530.9760.98698.00290.145
3.976-4.2490.168910.12318300.12519410.9840.99198.96960.12
4.249-4.5860.154860.11317090.11518220.9860.99298.51810.112
4.586-5.0190.142800.11315810.11516790.9870.99298.92790.118
5.019-5.6040.176690.1514060.15114920.9820.98798.86060.155
5.604-6.4560.208640.17912630.18113360.9780.98499.32630.18
6.456-7.8710.199540.17110660.17211330.9750.98398.85260.179
7.871-10.9820.234410.1758220.1788750.9730.98198.62860.192
10.982-47.670.288210.3264220.3245080.9390.93187.20470.45
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)
10.4625-0.0736-0.11450.25270.08431.47810.00550.21180.105-0.1154-0.05490.01320.1389-0.16770.04940.14510.0062-0.03220.1297-0.03790.3025-22.9557-7.8634-35.1782
24.2190.32530.36671.27410.31591.09170.03070.0858-0.1476-0.1262-0.0047-0.0640.04290.083-0.02610.12420.01260.03730.0092-0.01680.2898-23.1405-38.8115-22.1769
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAp876 - 1301
2X-RAY DIFFRACTION2ALLBp876 - 1301

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