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- PDB-5jpz: Crystal structure of HAT domain of human Squamous Cell Carcinoma ... -

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Basic information

Entry
Database: PDB / ID: 5jpz
TitleCrystal structure of HAT domain of human Squamous Cell Carcinoma Antigen Recognized By T Cells 3, SART3 (TIP110)
ComponentsSquamous cell carcinoma antigen recognized by T-cells 3
KeywordsRNA BINDING PROTEIN / half-a-tetratricopeptide repeat (HAT) domaiN / nuclear RNA-Binding Protein / mRNA splicing
Function / homology
Function and homology information


U6atac snRNA binding / ASAP complex / U4 snRNA binding / transcription elongation-coupled chromatin remodeling / hematopoietic stem cell proliferation / ubiquitin-specific protease binding / homeostasis of number of cells / spliceosomal tri-snRNP complex assembly / U6 snRNA binding / spliceosomal snRNP assembly ...U6atac snRNA binding / ASAP complex / U4 snRNA binding / transcription elongation-coupled chromatin remodeling / hematopoietic stem cell proliferation / ubiquitin-specific protease binding / homeostasis of number of cells / spliceosomal tri-snRNP complex assembly / U6 snRNA binding / spliceosomal snRNP assembly / Cajal body / cell morphogenesis / mRNA splicing, via spliceosome / nucleosome assembly / histone binding / regulation of gene expression / nuclear speck / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
SART3, RNA recognition motif 1 / SART3, RNA recognition motif 2 / LSM-interacting associated unstructured / LSM-interacting domain / Lsm interaction motif / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. ...SART3, RNA recognition motif 1 / SART3, RNA recognition motif 2 / LSM-interacting associated unstructured / LSM-interacting domain / Lsm interaction motif / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Tetratricopeptide-like helical domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Squamous cell carcinoma antigen recognized by T-cells 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.045 Å
AuthorsGrazette, A. / Harper, S. / Emsley, J. / Layfield, R. / Dreveny, I.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/H012656/1 United Kingdom
CitationJournal: To Be Published
Title: unpublished
Authors: Grazette, A. / Harper, S. / Emsley, J. / Oldham, N.J. / Layfield, R. / Dreveny, I.
History
DepositionMay 4, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_close_contact ...pdbx_data_processing_status / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Revision 1.3May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Squamous cell carcinoma antigen recognized by T-cells 3
B: Squamous cell carcinoma antigen recognized by T-cells 3


Theoretical massNumber of molelcules
Total (without water)120,2002
Polymers120,2002
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint10 kcal/mol
Surface area47080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.568, 118.351, 133.294
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 92:102 or (resid 103 and (name...
21(chain B and (resseq 92:102 or (resid 103 and (name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYGLUGLU(chain A and (resseq 92:102 or (resid 103 and (name...AA92 - 10227 - 37
12GLUGLUGLUGLU(chain A and (resseq 92:102 or (resid 103 and (name...AA10338
13GLYGLYALAALA(chain A and (resseq 92:102 or (resid 103 and (name...AA92 - 57427 - 509
14GLYGLYALAALA(chain A and (resseq 92:102 or (resid 103 and (name...AA92 - 57427 - 509
15GLYGLYALAALA(chain A and (resseq 92:102 or (resid 103 and (name...AA92 - 57427 - 509
16GLYGLYALAALA(chain A and (resseq 92:102 or (resid 103 and (name...AA92 - 57427 - 509
17GLYGLYALAALA(chain A and (resseq 92:102 or (resid 103 and (name...AA92 - 57427 - 509
18GLYGLYALAALA(chain A and (resseq 92:102 or (resid 103 and (name...AA92 - 57427 - 509
19GLYGLYALAALA(chain A and (resseq 92:102 or (resid 103 and (name...AA92 - 57427 - 509
21GLYGLYGLUGLU(chain B and (resseq 92:102 or (resid 103 and (name...BB92 - 10227 - 37
22GLUGLUGLUGLU(chain B and (resseq 92:102 or (resid 103 and (name...BB10338
23ALAALAALAALA(chain B and (resseq 92:102 or (resid 103 and (name...BB90 - 57425 - 509
24ALAALAALAALA(chain B and (resseq 92:102 or (resid 103 and (name...BB90 - 57425 - 509
25ALAALAALAALA(chain B and (resseq 92:102 or (resid 103 and (name...BB90 - 57425 - 509
26ALAALAALAALA(chain B and (resseq 92:102 or (resid 103 and (name...BB90 - 57425 - 509
27ALAALAALAALA(chain B and (resseq 92:102 or (resid 103 and (name...BB90 - 57425 - 509
28ALAALAALAALA(chain B and (resseq 92:102 or (resid 103 and (name...BB90 - 57425 - 509
29ALAALAALAALA(chain B and (resseq 92:102 or (resid 103 and (name...BB90 - 57425 - 509

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Components

#1: Protein Squamous cell carcinoma antigen recognized by T-cells 3 / SART-3 / Tat-interacting protein of 110 kDa / Tip110 / p110 nuclear RNA-binding protein


Mass: 60100.004 Da / Num. of mol.: 2 / Fragment: UNP residues 96-574
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SART3, KIAA0156, TIP110 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15020
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 3.65 Å3/Da / Density % sol: 66.28 %
Crystal growTemperature: 283.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M Monosaccharides; 0.1M Tris/Bicine (pH 7.3), 32%PEG550MME_PEG20K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.97372 Å
DetectorType: DECTRIS PILATUS3 X 1M / Detector: PIXEL / Date: Jun 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97372 Å / Relative weight: 1
ReflectionResolution: 3.04→59.18 Å / Num. obs: 32447 / % possible obs: 99.3 % / Redundancy: 4.8 % / Biso Wilson estimate: 29.61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.042 / Rrim(I) all: 0.093 / Net I/σ(I): 12.5 / Num. measured all: 155195
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.04-3.214.70.8421.7196.6
9.63-59.184.20.02545199.1

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Processing

Software
NameVersionClassification
Aimless0.5.25data scaling
PHENIXphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 3.045→56.356 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.16
RfactorNum. reflection% reflection
Rfree0.2801 1587 4.9 %
Rwork0.2361 --
obs0.2383 32380 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 110.84 Å2 / Biso mean: 45.414 Å2 / Biso min: 1.68 Å2
Refinement stepCycle: final / Resolution: 3.045→56.356 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8011 0 0 25 8036
Biso mean---33.13 -
Num. residues----968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118277
X-RAY DIFFRACTIONf_angle_d1.31111211
X-RAY DIFFRACTIONf_chiral_restr0.0671193
X-RAY DIFFRACTIONf_plane_restr0.0121450
X-RAY DIFFRACTIONf_dihedral_angle_d20.553139
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4045X-RAY DIFFRACTION14.179TORSIONAL
12B4045X-RAY DIFFRACTION14.179TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0445-3.14280.40961330.36642617275095
3.1428-3.25510.38081350.32432760289599
3.2551-3.38540.31321380.297627922930100
3.3854-3.53950.29581350.265727902925100
3.5395-3.72610.2831380.235727852923100
3.7261-3.95950.30381470.212627882935100
3.9595-4.26510.27041530.208227862939100
4.2651-4.69410.25931480.200528242972100
4.6941-5.37290.24161470.203128242971100
5.3729-6.76750.23731560.220228533009100
6.7675-56.36560.21541570.18272974313199
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)
14.5351.65511.70263.11043.45424.0803-0.97750.71822.4028-1.14830.5150.8971-2.1085-0.27240.33641.04320.04420.08690.4528-0.4657-0.3579-37.9672110.7109-11.0525
20.93680.10650.87291.3284-1.57613.55210.4552-0.3176-0.0753-0.121-0.6659-0.11660.63440.33030.18350.8286-0.3835-0.14740.4885-0.14880.3313-33.908897.254-0.2238
32.24410.55730.5222.35870.22373.227-0.1856-0.2007-0.6028-0.32180.3110.67860.8432-0.6829-0.10830.7151-0.34370.02940.66490.00640.6355-40.497386.774218.6958
41.65770.170.70321.6356-0.93262.3385-0.2838-0.6158-0.30090.39460.32730.6406-0.1011-0.63870.01310.63890.01110.2710.6703-0.1390.7754-46.379102.534226.7995
51.87693.1315-0.69316.01811.57963.1137-0.09060.3401-0.0569-0.59650.1357-0.06880.0089-0.0854-0.04450.52480.0843-0.03340.1099-0.08210.2137-19.45126.566314.6369
61.9785-0.18750.19252.96250.11391.45680.20710.13980.2452-0.535-0.0049-0.20110.44960.0361-0.1130.30620.099-0.00480.1791-0.0930.2446-15.8432151.403421.26
71.8971.13570.77473.51970.50422.8866-0.0205-0.27420.5332-0.1449-0.29520.5589-0.3025-0.2250.19320.21760.0236-0.08470.249-0.09310.2784-17.5403163.643131.1923
83.4179-0.6355-2.11790.61250.06455.97260.20580.30850.40990.129-0.28750.3271-0.08890.72330.01710.2698-0.06330.10120.3231-0.08650.2482-17.6061204.047351.389
90.1999-0.11740.03215.396-0.54540.45690.1645-0.08270.06850.2915-0.23260.3612-0.1118-0.05080.04290.3312-0.0690.00030.3588-0.130.2369-20.4404165.720440.7604
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 92 through 125 )A92 - 125
2X-RAY DIFFRACTION2chain 'A' and (resid 126 through 178 )A126 - 178
3X-RAY DIFFRACTION3chain 'A' and (resid 179 through 261 )A179 - 261
4X-RAY DIFFRACTION4chain 'A' and (resid 262 through 360 )A262 - 360
5X-RAY DIFFRACTION5chain 'A' and (resid 361 through 489 )A361 - 489
6X-RAY DIFFRACTION6chain 'A' and (resid 490 through 541 )A490 - 541
7X-RAY DIFFRACTION7chain 'A' and (resid 542 through 574 )A542 - 574
8X-RAY DIFFRACTION8chain 'B' and (resid 90 through 278 )B90 - 278
9X-RAY DIFFRACTION9chain 'B' and (resid 279 through 574 )B279 - 574

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