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- PDB-6wmg: Human Sun2 (500-717) -

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Basic information

Entry
Database: PDB / ID: 6wmg
TitleHuman Sun2 (500-717)
ComponentsSUN domain-containing protein 2
KeywordsSTRUCTURAL PROTEIN / LINC Complex
Function / homology
Function and homology information


structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex
Similarity search - Function
Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S21
Similarity search - Domain/homology
: / Small ribosomal subunit protein bS21
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCruz, V.E. / Schwartz, T.U.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)AR065484 United States
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Structural Analysis of Different LINC Complexes Reveals Distinct Binding Modes.
Authors: Cruz, V.E. / Esra Demircioglu, F. / Schwartz, T.U.
History
DepositionApr 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 18, 2023Group: 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: SUN domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6772
Polymers24,6381
Non-polymers391
Water2,342130
1
A: SUN domain-containing protein 2
hetero molecules

A: SUN domain-containing protein 2
hetero molecules

A: SUN domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0306
Polymers73,9133
Non-polymers1173
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area7680 Å2
ΔGint-49 kcal/mol
Surface area26220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.192, 79.192, 199.470
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-1027-

HOH

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Components

#1: Protein SUN domain-containing protein 2 / Protein unc-84 homolog B / Rab5-interacting protein / Rab5IP / Sad1/unc-84 protein-like 2


Mass: 24637.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUN2, FRIGG, KIAA0668, RAB5IP, UNC84B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UH99
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.44 Å3/Da / Density % sol: 49.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 14.5% PEG 3350, 0.2M sodium bromide, 0.1M potassium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→56.51 Å / Num. obs: 19072 / % possible obs: 99 % / Redundancy: 3.7 % / Biso Wilson estimate: 37.45 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.042 / Net I/σ(I): 24
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1319 / CC1/2: 0.652 / Rpim(I) all: 0.599 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DXT

4dxt


Resolution: 1.9→56.51 Å / SU ML: 0.2182 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.8269
RfactorNum. reflection% reflection
Rfree0.2225 1913 10.03 %
Rwork0.1751 --
obs0.1798 19072 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 54.11 Å2
Refinement stepCycle: LAST / Resolution: 1.9→56.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1528 0 1 131 1660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071586
X-RAY DIFFRACTIONf_angle_d0.90392167
X-RAY DIFFRACTIONf_chiral_restr0.0591237
X-RAY DIFFRACTIONf_plane_restr0.0057284
X-RAY DIFFRACTIONf_dihedral_angle_d18.1918216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.3211290.28591190X-RAY DIFFRACTION96.7
1.95-20.28261480.25051212X-RAY DIFFRACTION99.71
2-2.060.25361380.22881223X-RAY DIFFRACTION99.56
2.06-2.130.28521310.2241250X-RAY DIFFRACTION99.78
2.13-2.20.26131420.21131223X-RAY DIFFRACTION100
2.2-2.290.23651290.1921210X-RAY DIFFRACTION99.48
2.29-2.390.23711370.19681237X-RAY DIFFRACTION99.49
2.39-2.520.26951410.19741238X-RAY DIFFRACTION99.42
2.52-2.680.27861330.19431228X-RAY DIFFRACTION99.49
2.68-2.880.23211420.19181241X-RAY DIFFRACTION99.35
2.88-3.170.25941440.18851219X-RAY DIFFRACTION98.06
3.17-3.630.19061310.16241234X-RAY DIFFRACTION97.5
3.64-4.580.17861300.14261175X-RAY DIFFRACTION92.55
4.58-56.510.20781380.15741279X-RAY DIFFRACTION94.91
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)
15.31362502856-0.6719621844533.157186579694.93929102097-2.823131708423.790209487350.292888343932-0.578057738571-0.3752433739060.03635978045190.2381726525110.4952753668941.14059884232-1.38939640915-0.3980913043980.369719221385-0.06615090949370.03096715239310.4214302384180.04436112125130.412681374532-5.4740030055-48.09757693138.92575763343
23.15952163593-0.3285311091550.3740641866482.03917032164-0.2883300655353.091048302260.02187560853250.3647114071480.188086936304-0.1706976743790.00161864713919-0.16567671978-0.427850069398-0.00236672131265-0.02047939810990.385498120160.05195344425060.02788665799920.2785383105940.005142792907080.293775486944-3.85190341909-30.3477028852-18.1463832782
38.07877126285-0.4556086834731.901961964744.81175510181-0.5242755865746.23108800283-0.4611948882041.17626731819-0.0117041465456-0.4110887546280.3433882824510.982083291458-1.22599424447-0.64393374284-0.05761494452540.6885418346930.227480203457-0.02317520021360.6360386202-0.03859551250530.630883632569-19.7814385704-21.1234152694-16.7297972936
43.39181099816-0.3221938616990.2866764448532.55978555903-0.1333145660814.04025329941-0.084430306829-0.1286710331320.4252532882630.2167459872860.1590846518380.1616191384-0.825041498323-0.578729231219-0.07252515351930.4682821327320.1415787044950.01792825991710.282200800045-0.01212893339360.300349141171-9.53347401325-25.9940573306-11.2190657081
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 522 through 540 )
2X-RAY DIFFRACTION2chain 'A' and (resid 541 through 651 )
3X-RAY DIFFRACTION3chain 'A' and (resid 652 through 666 )
4X-RAY DIFFRACTION4chain 'A' and (resid 667 through 716 )

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