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

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Basic information

Entry
Database: PDB / ID: 7yye
TitleOrthorombic crystal structure of YTHDF1 YTH domain (G459N mutant) form I
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
MALONIC ACID / YTH domain-containing family protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,4596
Polymers93,2934
Non-polymers1662
Water7,909439
1
A: YTH domain-containing family protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3852
Polymers23,3231
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YTH domain-containing family protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4272
Polymers23,3231
Non-polymers1041
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)71.541, 74.497, 154.270
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 372 through 398 or resid 400...
21(chain B and (resid 372 through 398 or resid 400...
31(chain C and (resid 372 through 398 or resid 400...
41(chain D and (resid 372 through 398 or resid 400...

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
11LYSLYSSERSER(chain A and (resid 372 through 398 or resid 400...AA372 - 39813 - 39
12ASPASPHISHIS(chain A and (resid 372 through 398 or resid 400...AA400 - 40341 - 44
13SERSERTYRTYR(chain A and (resid 372 through 398 or resid 400...AA405 - 45846 - 99
14GLYGLYGLUGLU(chain A and (resid 372 through 398 or resid 400...AA472 - 552113 - 193
15GLNGLNASNASN(chain A and (resid 372 through 398 or resid 400...AA554 - 557195 - 198
21LYSLYSSERSER(chain B and (resid 372 through 398 or resid 400...BB372 - 39813 - 39
22ASPASPHISHIS(chain B and (resid 372 through 398 or resid 400...BB400 - 40341 - 44
23SERSERTYRTYR(chain B and (resid 372 through 398 or resid 400...BB405 - 45846 - 99
24GLYGLYGLUGLU(chain B and (resid 372 through 398 or resid 400...BB472 - 552113 - 193
25GLNGLNASNASN(chain B and (resid 372 through 398 or resid 400...BB554 - 557195 - 198
31LYSLYSSERSER(chain C and (resid 372 through 398 or resid 400...CC372 - 39813 - 39
32ASPASPHISHIS(chain C and (resid 372 through 398 or resid 400...CC400 - 40341 - 44
33SERSERTYRTYR(chain C and (resid 372 through 398 or resid 400...CC405 - 45846 - 99
34GLYGLYGLUGLU(chain C and (resid 372 through 398 or resid 400...CC472 - 552113 - 193
35GLNGLNASNASN(chain C and (resid 372 through 398 or resid 400...CC554 - 557195 - 198
41LYSLYSSERSER(chain D and (resid 372 through 398 or resid 400...DD372 - 39813 - 39
42ASPASPHISHIS(chain D and (resid 372 through 398 or resid 400...DD400 - 40341 - 44
43SERSERTYRTYR(chain D and (resid 372 through 398 or resid 400...DD405 - 45846 - 99
44GLYGLYGLUGLU(chain D and (resid 372 through 398 or resid 400...DD472 - 552113 - 193
45GLNGLNASNASN(chain D and (resid 372 through 398 or resid 400...DD554 - 557195 - 198

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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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / 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: 2.2 Å3/Da / Density % sol: 44.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 6-12% PEG3350, 0.2 M KSCN, 0.1 M malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9718 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: 0.9718 Å / Relative weight: 1
ReflectionResolution: 2→74.5 Å / Num. obs: 56587 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.041 / Rrim(I) all: 0.149 / Net I/σ(I): 12.7 / Num. measured all: 732507 / Scaling rejects: 2
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
2-2.0512.41.635106241210.6190.481.7011.7100
8.94-74.510.20.0575817400.9990.0160.05236.199.7

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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→42.889 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2147 2981 5.28 %
Rwork0.1729 53518 -
obs0.1751 56499 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.67 Å2 / Biso mean: 41.9752 Å2 / Biso min: 17.87 Å2
Refinement stepCycle: final / Resolution: 2→42.889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6043 0 11 439 6493
Biso mean--52.67 44.87 -
Num. residues----731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076230
X-RAY DIFFRACTIONf_angle_d0.878380
X-RAY DIFFRACTIONf_chiral_restr0.058860
X-RAY DIFFRACTIONf_plane_restr0.0061086
X-RAY DIFFRACTIONf_dihedral_angle_d17.543787
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3377X-RAY DIFFRACTION12.746TORSIONAL
12B3377X-RAY DIFFRACTION12.746TORSIONAL
13C3377X-RAY DIFFRACTION12.746TORSIONAL
14D3377X-RAY DIFFRACTION12.746TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2-2.03280.29061450.25392501
2.0328-2.06790.2721330.24232534
2.0679-2.10550.26871420.21792515
2.1055-2.1460.2931440.21032500
2.146-2.18980.24051840.20322476
2.1898-2.23740.24481480.19572533
2.2374-2.28940.20121290.18612493
2.2894-2.34670.21471380.18362534
2.3467-2.41010.23751300.17642544
2.4101-2.4810.25761370.17862532
2.481-2.56110.24361300.17962534
2.5611-2.65260.24311380.18652533
2.6526-2.75880.24941410.19112544
2.7588-2.88430.24041310.1842548
2.8843-3.03640.20231260.18282554
3.0364-3.22650.19751290.16872591
3.2265-3.47560.20351310.16562542
3.4756-3.82510.20181460.15892580
3.8251-4.37820.21461890.14042556
4.3782-5.51420.16381280.14422644
5.5142-42.8890.1921620.18462730
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)
19.04420.2321-0.05822.3754-0.29811.78320.0140.11190.5565-0.1916-0.0564-0.1235-0.31870.0320.05330.43770.03940.01590.29110.0880.29298.32524.642-20.5392
23.55760.98970.89682.74930.47423.1775-0.14040.3372-0.2153-0.31630.0629-0.13640.15570.05730.07870.28110.0150.04790.21690.00730.19445.3723-11.7974-21.861
34.5181.103-0.58092.29660.50441.4057-0.0594-0.14560.1543-0.0554-0.08370.1284-0.0032-0.09820.15470.25980.04210.00520.22430.01570.192-3.3454-4.8813-12.0594
48.9124-7.8165-2.07979.33361.95211.2292-0.00140.3188-0.2218-0.1552-0.1966-0.27930.24620.14320.23220.29150.02040.07230.32190.06030.277325.9383-13.045-12.8224
54.46892.54280.80371.66641.25243.03360.1525-0.3217-0.62220.2279-0.0191-0.28080.30270.1278-0.08930.2280.0363-0.00770.22180.0040.277618.551-40.6794-5.2306
66.4642.09164.19913.75-1.49445.3377-0.0795-0.00590.160.2033-0.00730.1829-0.2098-0.03430.08130.2370.04530.00270.2143-0.01660.253615.9449-25.5557-3.1551
76.90071.9943-2.24933.18-0.6014.3501-0.0630.0205-0.2035-0.12730.0261-0.01360.1805-0.19070.07040.223-0.0005-0.01710.1928-0.01760.177510.3209-36.301-7.9293
84.19531.5368-0.81975.2671-0.98565.66190.10560.35830.82020.6204-0.17640.6132-0.6621-0.62340.04650.27280.050.04510.32070.03150.34555.9905-28.3747-0.1027
93.63880.37351.75132.6281.58232.6037-0.03580.5286-0.2174-0.19330.0627-0.13280.11280.2764-0.03020.23440.01030.05050.3036-0.00260.255919.7031-39.4343-15.7879
108.8396-5.8782-0.62474.16760.63752.4573-0.1741-0.36990.20990.25070.269-0.1235-0.1166-0.1533-0.07490.28-0.0232-0.03290.27790.05230.290720.136-12.2815-1.2544
113.0591.04280.58142.5890.82972.320.07390.0964-0.3110.0132-0.03610.04710.1843-0.0679-0.04340.28750.0120.01420.2465-0.06050.3259-10.7588-51.8461-18.5848
122.74710.476-0.36633.08961.61333.14940.09240.0172-0.03230.0735-0.05850.20940.1214-0.0578-0.02470.2102-0.00890.00720.1978-0.01670.2742-12.2575-48.3058-10.7634
131.2726-0.25240.21247.8293-5.82944.29290.05580.4594-0.1571-0.8429-0.0750.02930.57960.1962-0.05890.3897-0.0029-0.05040.5828-0.1630.4667-25.2822-46.9797-36.2554
144.41421.79910.07224.16040.45881.7725-0.14260.26550.3409-0.46670.16420.651-0.3061-0.2391-0.0130.50920.0752-0.09880.4152-0.02210.3528-26.6232-21.2284-36.2276
153.73911.45210.65444.81151.27032.2752-0.004-0.2092-0.15790.0403-0.0221-0.0128-0.1524-0.11590.01330.27040.0636-0.01240.3291-0.05050.2301-20.9758-24.512-26.2885
163.71251.39041.03312.09310.97932.7703-0.18940.5898-0.1983-0.57440.2967-0.1226-0.45890.276-0.12070.4815-0.0161-0.02770.3793-0.08530.2373-14.6618-23.2468-40.7554
172.3325-0.00980.94956.0363-6.70639.8607-0.23070.0846-0.29130.0730.13760.35520.1184-0.46170.05740.30440.03450.01520.447-0.15210.5199-32.654-43.4488-24.9343
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 364 through 388 )A364 - 388
2X-RAY DIFFRACTION2chain 'A' and (resid 389 through 475 )A389 - 475
3X-RAY DIFFRACTION3chain 'A' and (resid 476 through 531 )A476 - 531
4X-RAY DIFFRACTION4chain 'A' and (resid 532 through 557 )A532 - 557
5X-RAY DIFFRACTION5chain 'B' and (resid 372 through 398 )B372 - 398
6X-RAY DIFFRACTION6chain 'B' and (resid 399 through 414 )B399 - 414
7X-RAY DIFFRACTION7chain 'B' and (resid 415 through 452 )B415 - 452
8X-RAY DIFFRACTION8chain 'B' and (resid 453 through 475 )B453 - 475
9X-RAY DIFFRACTION9chain 'B' and (resid 476 through 531 )B476 - 531
10X-RAY DIFFRACTION10chain 'B' and (resid 532 through 558 )B532 - 558
11X-RAY DIFFRACTION11chain 'C' and (resid 364 through 452 )C364 - 452
12X-RAY DIFFRACTION12chain 'C' and (resid 453 through 531 )C453 - 531
13X-RAY DIFFRACTION13chain 'C' and (resid 532 through 559 )C532 - 559
14X-RAY DIFFRACTION14chain 'D' and (resid 365 through 398 )D365 - 398
15X-RAY DIFFRACTION15chain 'D' and (resid 399 through 475 )D399 - 475
16X-RAY DIFFRACTION16chain 'D' and (resid 476 through 531 )D476 - 531
17X-RAY DIFFRACTION17chain 'D' and (resid 532 through 558 )D532 - 558

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