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- PDB-9i5a: Crystal structure of wild type perlecan region 3 construct I876-V... -

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Basic information

Entry
Database: PDB / ID: 9i5a
TitleCrystal structure of wild type perlecan region 3 construct I876-V1272 construct 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: 2.045 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)86,19511
Polymers85,3142
Non-polymers8819
Water8,107450
1
A: Basement membrane-specific heparan sulfate proteoglycan core protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0515
Polymers42,6571
Non-polymers3944
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)43,1436
Polymers42,6571
Non-polymers4865
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.637, 74.612, 78.769
Angle α, β, γ (deg.)74.384, 74.084, 79.729
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

Dom-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLYGLYAA876 - 12401 - 365
2CYSCYSBB876 - 12461 - 371

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: 42656.910 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / 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: 3.65 Å3/Da / Density % sol: 66.34 %
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: 2.04→47.32 Å / Num. obs: 75120 / % possible obs: 98.3 % / Redundancy: 3.6 % / CC1/2: 0.997 / Net I/σ(I): 9.7
Reflection shellResolution: 2.04→2.1 Å / Num. unique obs: 5453 / CC1/2: 0.669

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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: 2.045→46.244 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 9.395 / SU ML: 0.122 / Cross valid method: FREE R-VALUE / ESU R: 0.132 / ESU R Free: 0.126
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2086 2000 2.662 %
Rwork0.1777 73118 -
all0.178 --
obs-75118 98.343 %
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: 61.621 Å2
Baniso -1Baniso -2Baniso -3
1--2.89 Å20.819 Å21.058 Å2
2---1 Å2-2.239 Å2
3---3.065 Å2
Refinement stepCycle: LAST / Resolution: 2.045→46.244 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5635 0 58 450 6143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0125890
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165068
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.8068013
X-RAY DIFFRACTIONr_angle_other_deg0.5681.74411792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3495757
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.555545
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.80710867
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.75110279
X-RAY DIFFRACTIONr_chiral_restr0.080.2826
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027220
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021360
X-RAY DIFFRACTIONr_nbd_refined0.2010.21121
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2070.24899
X-RAY DIFFRACTIONr_nbtor_refined0.1720.22916
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.23053
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2418
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0960.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1990.230
X-RAY DIFFRACTIONr_nbd_other0.2220.284
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2010.222
X-RAY DIFFRACTIONr_mcbond_it3.0093.5963013
X-RAY DIFFRACTIONr_mcbond_other3.0083.5963013
X-RAY DIFFRACTIONr_mcangle_it4.626.4453763
X-RAY DIFFRACTIONr_mcangle_other4.6196.4463764
X-RAY DIFFRACTIONr_scbond_it4.0924.0052877
X-RAY DIFFRACTIONr_scbond_other4.0914.0062878
X-RAY DIFFRACTIONr_scangle_it6.3177.1964246
X-RAY DIFFRACTIONr_scangle_other6.3167.1964247
X-RAY DIFFRACTIONr_lrange_it9.33738.3456443
X-RAY DIFFRACTIONr_lrange_other9.31337.7546340
X-RAY DIFFRACTIONr_ncsr_local_group_10.1050.0510509
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.105180.05009
12BX-RAY DIFFRACTIONLocal ncs0.105180.05009
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
2.045-2.0980.3471450.30253060.30356630.8990.91696.25640.278
2.098-2.1550.271430.27352540.27354990.9360.93298.14510.244
2.155-2.2180.2791410.26251200.26253570.9320.9498.20790.23
2.218-2.2860.2461350.24149410.24151820.9540.95297.95450.207
2.286-2.360.2151300.2247880.2249970.9710.96298.41910.184
2.36-2.4430.2291300.21247040.21249040.960.96698.57260.178
2.443-2.5350.2361230.18445230.18547080.9680.97598.68310.152
2.535-2.6380.2361190.1743290.17245020.9660.9898.80050.145
2.638-2.7550.2131140.17241810.17343510.9710.98198.71290.148
2.755-2.8890.2091090.15939880.16141410.9740.98398.93750.141
2.889-3.0450.2021040.15938010.1639530.9770.98498.78570.146
3.045-3.2280.19990.15736030.15837410.9830.98698.95750.148
3.228-3.450.187910.15833450.15834750.9810.98798.87770.152
3.45-3.7250.194860.14731610.14832900.9760.98898.6930.148
3.725-4.0780.167790.14228790.14230000.9840.98898.60.147
4.078-4.5550.166710.13225960.13327090.9810.98998.44960.143
4.555-5.2510.177640.14623230.14724160.9810.98898.79970.163
5.251-6.410.228530.19519500.19620210.970.98199.10940.212
6.41-8.9790.21420.18915050.1915630.9770.9898.97630.213
8.979-46.2440.241220.2478210.2479060.9640.95693.04640.34
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)
10.6692-0.0756-0.13520.59770.23821.3954-0.00260.2060.0469-0.1335-0.05260.01390.0831-0.12190.05520.0442-0.00140.00020.0690.01950.1939-22.2946-7.9334-34.6696
23.72840.24670.05841.95930.34610.76990.00550.4568-0.0968-0.4292-0.0055-0.0986-0.01890.0854-00.09960.0150.01990.06970.01710.2162-21.185-39.5299-28.7409
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAp876 - 1305
2X-RAY DIFFRACTION2ALLBp876 - 1254

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