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- PDB-3h6n: Crystal Structure of the ubiquitin-like domain of plexin D1 -

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Basic information

Entry
Database: PDB / ID: 3h6n
TitleCrystal Structure of the ubiquitin-like domain of plexin D1
ComponentsPlexin-D1
KeywordsSIGNALING PROTEIN / structural genomics consortium / SGC / MEMBRANE / transmembrane / receptor / Alternative splicing / Cell membrane / Glycoprotein / Polymorphism
Function / homology
Function and homology information


dichotomous subdivision of terminal units involved in salivary gland branching / Other semaphorin interactions / synaptic target recognition / cardiac septum development / semaphorin receptor complex / coronary vasculature development / semaphorin receptor activity / negative regulation of cell adhesion / aorta development / RND2 GTPase cycle ...dichotomous subdivision of terminal units involved in salivary gland branching / Other semaphorin interactions / synaptic target recognition / cardiac septum development / semaphorin receptor complex / coronary vasculature development / semaphorin receptor activity / negative regulation of cell adhesion / aorta development / RND2 GTPase cycle / NOTCH3 Intracellular Domain Regulates Transcription / positive regulation of axonogenesis / branching involved in blood vessel morphogenesis / outflow tract morphogenesis / lamellipodium membrane / semaphorin-plexin signaling pathway / endothelial cell migration / regulation of angiogenesis / synapse assembly / regulation of cell migration / kidney development / lamellipodium / regulation of cell shape / cell body / angiogenesis / negative regulation of neuron apoptotic process / protein domain specific binding / axon / glutamatergic synapse / plasma membrane
Similarity search - Function
Plexin-D1, sema domain / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RasGAP domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RasGAP domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin family / Plexin repeat / Plexin repeat ...Plexin-D1, sema domain / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RasGAP domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RasGAP domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / IPT/TIG domain / ig-like, plexins, transcription factors / Rho GTPase activation protein / PSI domain / domain found in Plexins, Semaphorins and Integrins / IPT domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Immunoglobulin E-set / WD40/YVTN repeat-like-containing domain superfamily / Roll / Immunoglobulin-like fold / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.004 Å
AuthorsTong, Y. / Nedyalkova, L. / Tempel, W. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Buck, M. ...Tong, Y. / Nedyalkova, L. / Tempel, W. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Buck, M. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of the ubiquitin-like domain of plexin D1
Authors: Tong, Y. / Nedyalkova, L. / Tempel, W. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Buck, M. / Park, H.
History
DepositionApr 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plexin-D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6674
Polymers14,5171
Non-polymers1503
Water19811
1
A: Plexin-D1
hetero molecules

A: Plexin-D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3348
Polymers29,0342
Non-polymers3006
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2120 Å2
ΔGint-38 kcal/mol
Surface area10890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.777, 27.051, 52.653
Angle α, β, γ (deg.)90.00, 114.06, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Plexin-D1


Mass: 14516.962 Da / Num. of mol.: 1 / Fragment: ubiquitin-like domain (UNP residues 1553-1678)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLXND1, KIAA0620 / Plasmid: pET28-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: Q9Y4D7
#2: Chemical ChemComp-ARS / ARSENIC


Mass: 74.922 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: As
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE ELECTRON DENSITY SUGGESTS THE MODIFICATION OF THE SULFHYDRYL GROUPS OF CYS-1565 AND CYS-1592, ...THE ELECTRON DENSITY SUGGESTS THE MODIFICATION OF THE SULFHYDRYL GROUPS OF CYS-1565 AND CYS-1592, POSSIBLY BY A REACTION INVOLVING CACODYLATE, SIMILAR TO SCOTT ET AL (1993, CHEM RES TOXICOL 6:102) AND GOLDGUR ET AL (1998, PROC NATL ACAD SCI USA 95:9150). ONLY THE PUTATIVE ARSENIC ATOMS OF THE MODIFICATION HAVE BEEN MODELED.
Sequence detailsSOLVENT CONTENT AND MATTHEWS COEFFICIENT WERE CALCULATED BASED ON THE PURIFIED PROTEIN CONSTRUCT. ...SOLVENT CONTENT AND MATTHEWS COEFFICIENT WERE CALCULATED BASED ON THE PURIFIED PROTEIN CONSTRUCT. HOWEVER, THE PROTEASE ADDED FOR CRYSTALLIZATION MAY HAVE REDUCED THE CHAIN LENGTH OF THE TARGET PROTEIN.

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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: 2.3 Å3/Da / Density % sol: 46.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 1.39M sodium citrate, 0.1M sodium cacodylate. The protein stock solution was adjusted to contain 15 mM TCEP, supplemented with 1:100 (w/w) chymotrypsin, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97942 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 7245 / % possible obs: 99.5 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.086 / Χ2: 2.407 / Net I/σ(I): 9.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.033.60.4993811.3499.7
2.03-2.073.60.5533432.67199.4
2.07-2.114.10.4463571.21100
2.11-2.154.20.4163561.25299.7
2.15-2.24.40.3293651.173100
2.2-2.254.40.3833551.4498.3
2.25-2.314.60.33331.597100
2.31-2.374.70.2813781.247100
2.37-2.444.70.2083631.173100
2.44-2.524.70.1913601.46699.7
2.52-2.614.80.1733531.411100
2.61-2.714.70.1443761.52499.7
2.71-2.844.80.1193481.824100
2.84-2.994.70.1023642.05199.7
2.99-3.174.60.0943532.362100
3.17-3.424.60.0693712.53499.2
3.42-3.764.60.0683663.24298.7
3.76-4.314.40.0633564.298.1
4.31-5.424.20.0553834.44399.2
5.42-303.90.06938410.94598.5

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
DMphasing
REFMAC5.5.0072refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.004→30 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.887 / WRfactor Rfree: 0.27 / WRfactor Rwork: 0.239 / SU B: 11.569 / SU ML: 0.154 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED. Phenix, Arp/warp, Coot and Molprobity were also used during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.276 337 4.662 %RANDOM
Rwork0.243 ---
obs0.244 7229 98.865 %-
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: 31.154 Å2
Baniso -1Baniso -2Baniso -3
1--1.706 Å20 Å2-0.265 Å2
2--1.444 Å20 Å2
3---0.046 Å2
Refinement stepCycle: LAST / Resolution: 2.004→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms775 0 3 11 789
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022789
X-RAY DIFFRACTIONr_bond_other_d0.0020.02506
X-RAY DIFFRACTIONr_angle_refined_deg1.0951.961075
X-RAY DIFFRACTIONr_angle_other_deg0.7483.0031237
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0125103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44624.68832
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38915122
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.348154
X-RAY DIFFRACTIONr_chiral_restr0.0620.2126
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021892
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02154
X-RAY DIFFRACTIONr_mcbond_it0.9832519
X-RAY DIFFRACTIONr_mcbond_other0.2172207
X-RAY DIFFRACTIONr_mcangle_it1.6513825
X-RAY DIFFRACTIONr_scbond_it1.3052270
X-RAY DIFFRACTIONr_scangle_it1.8143250
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.004-2.0560.29180.34950555993.56
2.056-2.1120.264230.32246949599.394
2.112-2.1730.251210.30147049399.594
2.173-2.2390.365210.29447049798.793
2.239-2.3120.434230.2844046898.932
2.312-2.3930.291160.26244546299.784
2.393-2.4830.19200.23642945199.557
2.483-2.5830.229180.26339941999.523
2.583-2.6970.161180.26440642599.765
2.697-2.8280.271220.275361383100
2.828-2.9790.305200.26236538699.741
2.979-3.1580.3240.268336360100
3.158-3.3740.271130.24331733399.099
3.374-3.640.184130.22928930599.016
3.64-3.9820.298180.1927229598.305
3.982-4.4420.281130.18925827698.188
4.442-5.110.284120.17621422899.123
5.11-6.2140.236140.21419020599.512
6.214-8.6050.36450.27816317098.824
8.605-300.45350.3059410297.059
Refinement TLS params.Method: refined / Origin x: 16.5258 Å / Origin y: 16.6552 Å / Origin z: 14.8903 Å
111213212223313233
T0.0439 Å2-0.0152 Å20.0303 Å2-0.0751 Å2-0.0101 Å2--0.0843 Å2
L3.2374 °20.4764 °22.8561 °2-2.1422 °20.6545 °2--4.8958 °2
S-0.1521 Å °-0.0408 Å °-0.0478 Å °-0.1307 Å °0.0831 Å °0.0034 Å °0.1086 Å °-0.1199 Å °0.069 Å °

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