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- PDB-5fir: Crystal structure of C. elegans XRN2 in complex with the XRN2-bin... -

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Basic information

Entry
Database: PDB / ID: 5fir
TitleCrystal structure of C. elegans XRN2 in complex with the XRN2-binding domain of PAXT-1
Components
  • 5'-3' EXORIBONUCLEASE 2 HOMOLOG
  • PAXT-1
KeywordsHYDROLASE / 5'-3' EXORIBONUCLEASE / MIRNA TURNOVER
Function / homology
Function and homology information


Major pathway of rRNA processing in the nucleolus and cytosol / : / regulation of vulval development / regulation of development, heterochronic / negative regulation of miRNA-mediated gene silencing / miRNA catabolic process / 5'-3' RNA exonuclease activity / multicellular organism development / 5'-3' exonuclease activity / nuclear-transcribed mRNA catabolic process ...Major pathway of rRNA processing in the nucleolus and cytosol / : / regulation of vulval development / regulation of development, heterochronic / negative regulation of miRNA-mediated gene silencing / miRNA catabolic process / 5'-3' RNA exonuclease activity / multicellular organism development / 5'-3' exonuclease activity / nuclear-transcribed mRNA catabolic process / DNA-templated transcription termination / mRNA processing / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / nucleolus / RNA binding / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
XRN2-binding (XTBD) domain / XRN-Two Binding Domain, XTBD / XRN2-binding (XTBD) domain profile. / 5'-3' exoribonuclease type 2 / Xrn1, N-terminal / 5'-3' exoribonuclease / Xrn1, helical domain / XRN 5'-3' exonuclease N-terminus / Xrn1 helical domain
Similarity search - Domain/homology
Partner of xrn-2 protein 1 / 5'-3' exoribonuclease 2 homolog
Similarity search - Component
Biological speciesCAENORHABDITIS ELEGANS (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.836 Å
AuthorsRichter, H. / Katic, I. / Gut, H. / Grosshans, H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Structural Basis and Function of Xrn2-Binding by Xtb Domains
Authors: Richter, H. / Katic, I. / Gut, H. / Grosshans, H.
History
DepositionOct 2, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Mar 2, 2016Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: 5'-3' EXORIBONUCLEASE 2 HOMOLOG
B: PAXT-1
C: 5'-3' EXORIBONUCLEASE 2 HOMOLOG
D: PAXT-1
E: 5'-3' EXORIBONUCLEASE 2 HOMOLOG
F: PAXT-1
G: 5'-3' EXORIBONUCLEASE 2 HOMOLOG
H: PAXT-1
I: 5'-3' EXORIBONUCLEASE 2 HOMOLOG
J: PAXT-1
K: 5'-3' EXORIBONUCLEASE 2 HOMOLOG
L: PAXT-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)505,98139
Polymers503,38812
Non-polymers2,59427
Water95553
1
A: 5'-3' EXORIBONUCLEASE 2 HOMOLOG
B: PAXT-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,66610
Polymers83,8982
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-93.9 kcal/mol
Surface area31880 Å2
MethodPISA
2
C: 5'-3' EXORIBONUCLEASE 2 HOMOLOG
D: PAXT-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,1865
Polymers83,8982
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-53.7 kcal/mol
Surface area30620 Å2
MethodPISA
3
E: 5'-3' EXORIBONUCLEASE 2 HOMOLOG
F: PAXT-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,3787
Polymers83,8982
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-59.9 kcal/mol
Surface area30660 Å2
MethodPISA
4
G: 5'-3' EXORIBONUCLEASE 2 HOMOLOG
H: PAXT-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,2826
Polymers83,8982
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-64.1 kcal/mol
Surface area30880 Å2
MethodPISA
5
I: 5'-3' EXORIBONUCLEASE 2 HOMOLOG
J: PAXT-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,1865
Polymers83,8982
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-49.1 kcal/mol
Surface area30710 Å2
MethodPISA
6
K: 5'-3' EXORIBONUCLEASE 2 HOMOLOG
L: PAXT-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,2826
Polymers83,8982
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-64.4 kcal/mol
Surface area31050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.210, 200.770, 202.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.2005, -0.08958, 0.9756), (-0.9767, -0.05977, -0.2062), (0.07678, -0.9942, -0.0755)86.17, 209.4, 94.64
2given(0.08585, -0.9962, 0.01665), (0.1821, -0.000739, -0.9833), (0.97955, 0.08745, 0.1814)157.1, 90.09, -97.62
3given(0.01323, -0.9958, 0.09106), (0.9864, 0.02793, 0.1621), (-0.164, 0.08767, 0.9826)200.5, -47.47, -44.56
4given(-0.9891, 0.06433, -0.1327), (0.1322, -0.01256, -0.9911), (-0.06543, -0.9978, 0.00392)228.5, 139.2, 160.9
5given(-0.2545, -0.00338, 0.9671), (-0.02477, 0.9997, -0.003026), (-0.9667, -0.02473, -0.2545)46.48, -40.46, 166.7
6given(-0.2128, -0.17, 0.9622), (-0.9749, -0.02958, -0.2208), (0.06601, -0.985, -0.1594)92.28, 208.7, 102.3
7given(0.06128, -0.9976, -0.03204), (0.2089, 0.04421, -0.9769), (0.976, 0.05317, 0.2111)164.1, 84.52, -97.71
8given(0.01486, -0.9985, 0.05245), (0.9863, 0.02326, 0.1634), (-0.1643, 0.04931, 0.9852)203.6, -47.73, -43.44
9given(-0.9844, 0.1267, -0.1224), (0.1264, 0.02413, -0.9917), (-0.1227, -0.9916, -0.03977)223.7, 138.1, 171.1
10given(-0.2643, -0.03721, 0.9637), (0.008807, 0.9991, 0.04099), (-0.9644, 0.01932, -0.2637)49.36, -48.06, 164.8

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Components

#1: Protein
5'-3' EXORIBONUCLEASE 2 HOMOLOG


Mass: 74909.094 Da / Num. of mol.: 6 / Fragment: RESIDUES 1-257,295-417,532-787
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAENORHABDITIS ELEGANS (invertebrata) / Gene: XRN-2, Y48B6A.3 / Plasmid: PCOLADUET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9U299, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: Protein
PAXT-1


Mass: 8988.857 Da / Num. of mol.: 6 / Fragment: XTBD, RESIDUES 2-75
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAENORHABDITIS ELEGANS (invertebrata) / Gene: PAXT-1, CELE_R05D11.6, R05D11.6 / Plasmid: PCOLADUET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q21738
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE XRN2 CONSTRUCT CONSISTS OF RESIDUES 1-257, 295-417, 532-787. NOT INCLUDED ARE RESIDUES 258-294, ...THE XRN2 CONSTRUCT CONSISTS OF RESIDUES 1-257, 295-417, 532-787. NOT INCLUDED ARE RESIDUES 258-294, 418-531, 788- 975. RESIDUES GGGR IN THE PAXT-1 CONSTRUCT COME FROM THE EXPRESSION PLASMID AFTER PROTEOLYTIC CLEAVAGE OF THE 6HIS- TAG.

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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: 3.45 Å3/Da / Density % sol: 64.3 % / Description: NONE
Crystal growDetails: 2M AMMONIUM SULFATE, 0.1 M BIS-TRIS PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97796
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97796 Å / Relative weight: 1
ReflectionResolution: 2.84→50 Å / Num. obs: 155519 / % possible obs: 94.6 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 72.49 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.1
Reflection shellResolution: 2.84→2.91 Å / Redundancy: 3.1 % / Rmerge(I) obs: 1.26 / Mean I/σ(I) obs: 0.75 / % possible all: 84.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HOMOLOGY MODEL

Resolution: 2.836→49.393 Å / SU ML: 0.49 / σ(F): 1.35 / Phase error: 27.42 / Stereochemistry target values: ML
Details: PAXT-1 CHAINS H,J,L ARE PARTIALLY DISORDERED OR NOT FULLY OCCUPIED IN THE CRYSTAL. THEY WERE MODELED STEREOCHEMICALLY USING NCS RESTRAINTS.
RfactorNum. reflection% reflection
Rfree0.2376 3902 2.5 %
Rwork0.1854 --
obs0.1867 155484 94.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86 Å2
Refinement stepCycle: LAST / Resolution: 2.836→49.393 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33342 0 135 53 33530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01134354
X-RAY DIFFRACTIONf_angle_d1.1846576
X-RAY DIFFRACTIONf_dihedral_angle_d14.66320652
X-RAY DIFFRACTIONf_chiral_restr0.0634857
X-RAY DIFFRACTIONf_plane_restr0.0086103
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8364-2.8710.42511270.37174012X-RAY DIFFRACTION71
2.871-2.90730.39231520.36365476X-RAY DIFFRACTION97
2.9073-2.94560.39751270.35425517X-RAY DIFFRACTION97
2.9456-2.98590.37011480.3395460X-RAY DIFFRACTION96
2.9859-3.02860.34931390.33525489X-RAY DIFFRACTION97
3.0286-3.07380.42351360.34055477X-RAY DIFFRACTION97
3.0738-3.12180.33231370.31945466X-RAY DIFFRACTION96
3.1218-3.17290.3591410.29435485X-RAY DIFFRACTION96
3.1729-3.22770.33191290.26425488X-RAY DIFFRACTION97
3.2277-3.28630.29171450.24725508X-RAY DIFFRACTION97
3.2863-3.34950.27871410.23595433X-RAY DIFFRACTION96
3.3495-3.41790.28611400.2265485X-RAY DIFFRACTION96
3.4179-3.49220.28591350.21815489X-RAY DIFFRACTION96
3.4922-3.57340.25881460.20015496X-RAY DIFFRACTION96
3.5734-3.66270.24441390.19195512X-RAY DIFFRACTION97
3.6627-3.76170.24281430.17585506X-RAY DIFFRACTION96
3.7617-3.87240.22981430.1685430X-RAY DIFFRACTION96
3.8724-3.99730.2041390.1565473X-RAY DIFFRACTION96
3.9973-4.14010.19991420.14515479X-RAY DIFFRACTION95
4.1401-4.30580.22571370.14415479X-RAY DIFFRACTION96
4.3058-4.50160.19761410.1325466X-RAY DIFFRACTION95
4.5016-4.73880.16421430.12655413X-RAY DIFFRACTION94
4.7388-5.03540.18891460.1355464X-RAY DIFFRACTION95
5.0354-5.42380.21351400.14625455X-RAY DIFFRACTION95
5.4238-5.96870.21711410.16185443X-RAY DIFFRACTION94
5.9687-6.83050.23031360.16965449X-RAY DIFFRACTION93
6.8305-8.59830.19361300.16825404X-RAY DIFFRACTION92
8.5983-49.40090.19411390.15785328X-RAY DIFFRACTION88
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)
11.4380.1957-0.42083.1865-0.78311.5248-0.12140.15230.19320.25780.01760.33-0.2349-0.1480.10820.4387-0.01310.07990.53340.03230.5876100.79829.06286.4245
22.3903-1.9052-0.76522.0186-0.86857.62220.03690.65120.1378-0.3728-0.3706-0.54430.13550.14270.3020.7701-0.27920.05050.84840.28960.9736122.959450.873769.388
31.4480.16110.92391.9201-0.27211.8808-0.03580.096-0.1933-0.01720.06350.13860.036-0.0347-0.02660.2639-0.04790.09020.5240.06330.4989147.638791.463266.9307
47.53430.13530.72696.65340.6765.7411-0.21480.2718-0.095-0.32660.19251.10030.6705-0.8672-0.04760.725-0.2577-0.23340.7688-0.01240.97124.546472.061549.1899
52.2114-0.80240.20241.30120.34241.1835-0.1069-0.0555-0.0231-0.00380.04340.3466-0.0804-0.24570.03050.40640.0284-0.10780.4963-0.04830.5275138.282723.483919.2627
60.81240.31871.96236.76680.21545.025-0.5658-0.43540.37880.12340.10150.4128-0.6754-0.72080.3810.71120.26020.05781.0439-0.28411.0428118.608144.714439.6637
72.940.96580.7651.86820.21190.8296-0.20650.36540.3765-0.36880.08430.4695-0.202-0.07510.07160.4704-0.0255-0.0620.55990.04390.419180.678666.65826.3322
81.6533-0.13792.45040.8928-1.61555.8537-0.23370.91710.961-0.919-0.18010.6472-0.59150.00620.25881.36640.2156-0.68441.39310.37791.8863158.312986.05857.6731
91.0462-0.0693-0.23862.008-0.59132.51310.04630.42550.2794-0.8704-0.0409-0.1498-0.21340.0321-0.01720.86560.04490.10890.62780.12840.5289119.261366.5538125.7031
104.92650.8102-0.13453.50461.1550.43820.37531.11320.8993-0.53480.16380.4353-0.3067-0.4941-0.50812.03990.2801-0.33991.47990.53161.193100.613384.9529102.5973
111.0798-0.6073-0.49332.6851.10431.9270.25140.34230.0719-0.5197-0.31890.4822-0.3542-0.4431-0.01580.45390.1629-0.09170.7008-0.04610.6328104.2946-14.099146.5902
126.3641-1.3690.54541.43650.56710.46030.0880.17020.4241-0.5104-0.12550.4885-0.5498-1.04980.02441.63520.7659-0.43381.77430.13451.514782.25986.705228.8841
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN 'A' AND RESID 4 THROUGH 787)
2X-RAY DIFFRACTION2(CHAIN 'B' AND RESID 1 THROUGH 73)
3X-RAY DIFFRACTION3(CHAIN 'C' AND RESID 4 THROUGH 787)
4X-RAY DIFFRACTION4(CHAIN 'D' AND RESID 2 THROUGH 72)
5X-RAY DIFFRACTION5(CHAIN 'E' AND RESID 4 THROUGH 787)
6X-RAY DIFFRACTION6(CHAIN 'F' AND RESID 1 THROUGH 72)
7X-RAY DIFFRACTION7(CHAIN 'G' AND RESID 4 THROUGH 787)
8X-RAY DIFFRACTION8(CHAIN 'H' AND RESID 3 THROUGH 71)
9X-RAY DIFFRACTION9(CHAIN 'I' AND RESID 4 THROUGH 787)
10X-RAY DIFFRACTION10(CHAIN 'J' AND RESID 6 THROUGH 72)
11X-RAY DIFFRACTION11(CHAIN 'K' AND RESID 4 THROUGH 787)
12X-RAY DIFFRACTION12(CHAIN 'L' AND RESID 3 THROUGH 71)

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