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- PDB-7yyf: Orthorombic crystal structure of YTHDF1 YTH domain (G459N mutant)... -

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Basic information

Entry
Database: PDB / ID: 7yyf
TitleOrthorombic crystal structure of YTHDF1 YTH domain (G459N mutant) form II
ComponentsYTH domain-containing family protein 1
KeywordsRNA BINDING PROTEIN / mRNA binding and stability
Function / homology
Function and homology information


regulation of antigen processing and presentation / regulation of axon guidance / organelle assembly / N6-methyladenosine-containing RNA reader activity / regulation of long-term synaptic potentiation / immune system process / mRNA destabilization / positive regulation of translational initiation / stress granule assembly / regulation of mRNA stability ...regulation of antigen processing and presentation / regulation of axon guidance / organelle assembly / N6-methyladenosine-containing RNA reader activity / regulation of long-term synaptic potentiation / immune system process / mRNA destabilization / positive regulation of translational initiation / stress granule assembly / regulation of mRNA stability / learning / positive regulation of translation / P-body / memory / cytoplasmic stress granule / ribosome binding / mRNA binding / RNA binding / cytoplasm
Similarity search - Function
YTH domain containing protein / YTH domain / YT521-B-like domain / YTH domain profile.
Similarity search - Domain/homology
YTH domain-containing family protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsDalle Vedove, A. / Cazzanelli, G. / Lolli, G.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Association for Cancer ResearchMFAG 2017 - ID. 19882 Italy
CitationJournal: J.Chem.Inf.Model. / Year: 2024
Title: Pliability in the m 6 A-Binding Region Extends Druggability of YTH Domains.
Authors: Cazzanelli, G. / Dalle Vedove, A. / Spagnolli, G. / Terruzzi, L. / Colasurdo, E. / Boldrini, A. / Patsilinakos, A. / Sturlese, M. / Grottesi, A. / Biasini, E. / Provenzani, A. / Quattrone, A. / Lolli, G.
History
DepositionFeb 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
Revision 1.2Mar 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YTH domain-containing family protein 1
B: YTH domain-containing family protein 1
C: YTH domain-containing family protein 1
D: YTH domain-containing family protein 1


Theoretical massNumber of molelcules
Total (without water)93,2934
Polymers93,2934
Non-polymers00
Water3,045169
1
A: YTH domain-containing family protein 1


Theoretical massNumber of molelcules
Total (without water)23,3231
Polymers23,3231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YTH domain-containing family protein 1


Theoretical massNumber of molelcules
Total (without water)23,3231
Polymers23,3231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: YTH domain-containing family protein 1


Theoretical massNumber of molelcules
Total (without water)23,3231
Polymers23,3231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: YTH domain-containing family protein 1


Theoretical massNumber of molelcules
Total (without water)23,3231
Polymers23,3231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.126, 83.289, 123.815
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 (resid 364 through 403 or resid 405 through 458 or resid 472 through 558))
21(chain B and (resid 364 through 403 or resid 405 through 458 or resid 472 through 558))
31(chain C and (resid 364 through 403 or resid 405 through 458 or resid 472 through 558))
41(chain D and (resid 364 through 403 or resid 405 through 458 or resid 472 through 558))

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
11SERSERHISHIS(chain A and (resid 364 through 403 or resid 405 through 458 or resid 472 through 558))AA364 - 4035 - 44
12SERSERTYRTYR(chain A and (resid 364 through 403 or resid 405 through 458 or resid 472 through 558))AA405 - 45846 - 99
13GLYGLYLYSLYS(chain A and (resid 364 through 403 or resid 405 through 458 or resid 472 through 558))AA472 - 558113 - 199
21SERSERHISHIS(chain B and (resid 364 through 403 or resid 405 through 458 or resid 472 through 558))BB364 - 4035 - 44
22SERSERTYRTYR(chain B and (resid 364 through 403 or resid 405 through 458 or resid 472 through 558))BB405 - 45846 - 99
23GLYGLYLYSLYS(chain B and (resid 364 through 403 or resid 405 through 458 or resid 472 through 558))BB472 - 558113 - 199
31SERSERHISHIS(chain C and (resid 364 through 403 or resid 405 through 458 or resid 472 through 558))CC364 - 4035 - 44
32SERSERTYRTYR(chain C and (resid 364 through 403 or resid 405 through 458 or resid 472 through 558))CC405 - 45846 - 99
33GLYGLYLYSLYS(chain C and (resid 364 through 403 or resid 405 through 458 or resid 472 through 558))CC472 - 558113 - 199
41SERSERHISHIS(chain D and (resid 364 through 403 or resid 405 through 458 or resid 472 through 558))DD364 - 4035 - 44
42SERSERTYRTYR(chain D and (resid 364 through 403 or resid 405 through 458 or resid 472 through 558))DD405 - 45846 - 99
43GLYGLYLYSLYS(chain D and (resid 364 through 403 or resid 405 through 458 or resid 472 through 558))DD472 - 558113 - 199

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Components

#1: Protein
YTH domain-containing family protein 1 / DF1 / Dermatomyositis associated with cancer putative autoantigen 1 / DACA-1


Mass: 23323.219 Da / Num. of mol.: 4 / Fragment: YTH domain (residues 361-559)
Mutation: First residue G derives from the expression tag: G459N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YTHDF1, C20orf21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9BYJ9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.24 Å3/Da / Density % sol: 45.14 % / Mosaicity: 0.17 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 6-12% PEG3350, 0.2 M KSCN

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9717 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9717 Å / Relative weight: 1
ReflectionResolution: 2.3→69.11 Å / Num. obs: 37685 / % possible obs: 99.3 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.031 / Rrim(I) all: 0.114 / Net I/σ(I): 16.3 / Num. measured all: 487980 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.3812.81.2664644936350.7160.3661.3192.298.6
8.91-69.1110.40.0475317250.9980.0120.04245.797.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.11.1refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RCI

4rci


Resolution: 2.3→42.371 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2198 1826 4.85 %
Rwork0.1769 35804 -
obs0.1791 37630 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.25 Å2 / Biso mean: 55.2645 Å2 / Biso min: 24.5 Å2
Refinement stepCycle: final / Resolution: 2.3→42.371 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6120 0 0 169 6289
Biso mean---50.42 -
Num. residues----739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086275
X-RAY DIFFRACTIONf_angle_d0.9398434
X-RAY DIFFRACTIONf_chiral_restr0.058868
X-RAY DIFFRACTIONf_plane_restr0.0071086
X-RAY DIFFRACTIONf_dihedral_angle_d17.3693816
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3621X-RAY DIFFRACTION13.119TORSIONAL
12B3621X-RAY DIFFRACTION13.119TORSIONAL
13C3621X-RAY DIFFRACTION13.119TORSIONAL
14D3621X-RAY DIFFRACTION13.119TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.36220.31521320.2517270199
2.3622-2.43170.3121380.2327271199
2.4317-2.51020.27351270.2184270399
2.5102-2.59990.28931330.2153272699
2.5999-2.7040.28941490.2254269999
2.704-2.8270.28671400.2249273399
2.827-2.9760.321480.2099273999
2.976-3.16240.26271500.2038270599
3.1624-3.40650.2111280.1857277599
3.4065-3.74910.23971530.1818276199
3.7491-4.29120.18621230.153281599
4.2912-5.40470.18351320.13512824100
5.4047-42.3710.15341730.1558291299
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)
17.294-0.99862.45148.4766-2.21138.73620.18230.46450.6945-0.8801-0.01331.1091-1.28990.0125-0.29440.7508-0.0462-0.080.37460.07790.667-12.649917.5096-10.0019
22.73960.5367-0.52233.434-1.32314.3510.0681-0.09550.26240.1021-0.01070.058-0.14270.0105-0.06120.22430.03140.00270.2462-0.03980.3452-9.79791.30523.6305
32.1229-2.5964-2.85366.34562.93774.31040.0349-0.2290.8419-0.05310.3603-0.53680.03020.474-0.39130.31910.0037-0.01810.3609-0.03170.3881-2.81712.0145-0.7816
45.53531.85430.47263.9965-1.15854.17070.02120.4025-1.0801-0.91280.09150.01560.2483-0.7257-0.06050.3996-0.01060.00070.4565-0.0680.6087-19.4603-4.1519-1.6148
54.2464-0.80840.49963.7234-1.74854.01980.0468-0.05790.06430.108-0.1235-0.3335-0.14280.59980.0830.2638-0.0440.00410.3411-0.08350.29142.44031.635.502
67.25275.19766.46798.46595.92588.9865-0.11580.60980.0086-0.43980.15130.288-0.02230.3102-0.00740.47920.06330.01370.46320.05780.4054-13.23041.7583-21.2709
75.8912-1.06030.52638.6299-1.74752.72790.0658-0.6952-0.50481.13520.4592-0.09110.86361.0835-0.47450.72680.2363-0.11330.72180.07910.4098-6.4426-29.914342.2154
83.9201-2.0691.69146.4148-3.75955.3084-0.3218-0.9220.22221.22690.0161-0.2651-0.367-0.45450.32510.5867-0.0695-0.05660.5388-0.08280.3393-14.7274-11.378535.2247
96.27795.741-0.35659.6982-6.13197.1072-0.3618-0.1627-0.4704-0.55240.3741-0.71740.66170.62850.00450.3550.0742-0.01710.4391-0.01970.3029-12.9521-20.989719.7409
101.16550.8635-0.91625.563-3.52782.4712-0.0521-0.2883-0.5538-0.05610.1814-0.130.80760.6363-0.01660.44920.1161-0.0430.52170.06770.4602-6.4142-28.554326.3139
119.56020.6880.87587.9485-1.43474.8815-0.67341.0595-0.1542-1.03340.42820.0487-0.02090.77550.02990.2964-0.02540.04120.496-0.00420.27-3.7195-15.296315.1867
124.42350.90010.58965.8331-0.29555.02730.0683-0.4549-0.00920.0418-0.2446-0.4158-0.20510.42580.1510.25510.0201-0.03220.371-0.00270.2523-12.5723-17.739825.0466
133.22990.41270.4872.18680.37363.39780.53540.8662-0.161-0.2286-0.1778-1.57010.59340.3691-0.19040.40840.0795-0.01080.85260.02460.57950.58-22.738421.0766
143.14570.10090.54543.629-1.09624.3958-0.0536-0.20140.04120.0090.08510.1976-0.0787-0.2683-0.04860.28280.01360.00780.335-0.03740.285-21.6519-17.205724.5723
157.6394-5.9485-4.13165.65144.42775.5214-0.5554-0.3913-0.77570.55770.41330.15040.7560.84220.15150.590.1246-0.02410.55820.09040.5332-3.9586-42.66427.8473
162.09610.728-1.99179.8943-1.20561.96440.37391.55350.214-1.9811-0.2916-0.7153-0.84290.3230.02510.8662-0.02610.07710.83990.01340.4964-0.2036-12.278-35.769
172.862-0.3131-0.48915.2636-3.24072.49450.20560.5224-0.3038-0.8484-0.26250.11920.43120.0390.03410.39080.049-0.02760.4633-0.11840.3518-10.0544-26.92-23.9884
183.2879-0.77250.32044.1029-1.49753.1531-0.04390.0036-0.09990.048-0.11570.24650.046-0.0440.13480.24810.00470.0320.3466-0.06540.3096-5.1933-21.0924-16.7984
193.6843-0.14480.14222.9991-0.95363.2740.03040.1255-0.0522-0.2029-0.02580.6009-0.1276-0.3628-0.02750.35590.0088-0.05570.3376-0.1030.427-14.2121-23.8593-18.9817
203.32864.50122.9177.60956.04167.194-0.06390.26860.1653-0.40260.2618-0.1507-0.28430.4924-0.21880.50780.04050.04890.49310.05930.47580.27980.5889-21.1561
212.1973-0.4058-0.07724.6959-1.87661.4765-0.39580.0644-0.6691-0.25740.28470.24431.5651-0.07160.15361.0284-0.09190.1040.4386-0.1110.6898-9.3766-56.28913.5695
223.2211-0.47590.14463.7494-2.1997.2738-0.3304-0.1761-0.00870.27070.20550.21410.2113-0.19020.08480.3546-0.03740.06780.2929-0.03550.3838-12.5673-38.67275.6992
233.0199-0.76410.57674.6131-0.73047.2348-0.03040.2246-0.4345-0.14950.14840.27650.30110.178-0.04020.387-0.02460.0640.3698-0.02160.4779-7.0159-43.5011.8891
244.60531.51320.57254.4223-1.36385.6847-0.2123-0.1261-0.12360.03210.0526-0.29810.58310.65240.15990.38170.05890.07850.3697-0.05390.3756-2.0734-42.76372.5367
256.5582-4.3387-5.42735.04394.17995.1827-0.5096-0.2821-0.39010.46870.00440.2650.81030.21020.49950.73210.01610.08790.42360.11210.4901-17.6682-43.660826.127
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 364 through 374 )A364 - 374
2X-RAY DIFFRACTION2chain 'A' and (resid 375 through 440 )A375 - 440
3X-RAY DIFFRACTION3chain 'A' and (resid 441 through 452 )A441 - 452
4X-RAY DIFFRACTION4chain 'A' and (resid 453 through 475 )A453 - 475
5X-RAY DIFFRACTION5chain 'A' and (resid 476 through 531 )A476 - 531
6X-RAY DIFFRACTION6chain 'A' and (resid 532 through 558 )A532 - 558
7X-RAY DIFFRACTION7chain 'B' and (resid 364 through 374 )B364 - 374
8X-RAY DIFFRACTION8chain 'B' and (resid 375 through 389 )B375 - 389
9X-RAY DIFFRACTION9chain 'B' and (resid 390 through 398 )B390 - 398
10X-RAY DIFFRACTION10chain 'B' and (resid 399 through 414 )B399 - 414
11X-RAY DIFFRACTION11chain 'B' and (resid 415 through 427 )B415 - 427
12X-RAY DIFFRACTION12chain 'B' and (resid 428 through 452 )B428 - 452
13X-RAY DIFFRACTION13chain 'B' and (resid 453 through 475 )B453 - 475
14X-RAY DIFFRACTION14chain 'B' and (resid 476 through 531 )B476 - 531
15X-RAY DIFFRACTION15chain 'B' and (resid 532 through 558 )B532 - 558
16X-RAY DIFFRACTION16chain 'C' and (resid 364 through 374 )C364 - 374
17X-RAY DIFFRACTION17chain 'C' and (resid 375 through 398 )C375 - 398
18X-RAY DIFFRACTION18chain 'C' and (resid 399 through 452 )C399 - 452
19X-RAY DIFFRACTION19chain 'C' and (resid 453 through 531 )C453 - 531
20X-RAY DIFFRACTION20chain 'C' and (resid 532 through 558 )C532 - 558
21X-RAY DIFFRACTION21chain 'D' and (resid 364 through 389 )D364 - 389
22X-RAY DIFFRACTION22chain 'D' and (resid 390 through 427 )D390 - 427
23X-RAY DIFFRACTION23chain 'D' and (resid 428 through 452 )D428 - 452
24X-RAY DIFFRACTION24chain 'D' and (resid 453 through 531 )D453 - 531
25X-RAY DIFFRACTION25chain 'D' and (resid 532 through 558 )D532 - 558

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