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- PDB-6pi7: Crystal structure of the TDRD2 extended Tudor domain in complex w... -

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Basic information

Entry
Database: PDB / ID: 6pi7
TitleCrystal structure of the TDRD2 extended Tudor domain in complex with an antibody fragment and the PIWIL1 peptide
Components
  • Fab antigen-binding fragment
  • Piwi-like protein 1
  • Tudor and KH domain-containing protein
  • Uncharacterized protein
KeywordsPROTEIN BINDING / Fab / TUDOR domain / PIWIL1 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


piP-body / primary piRNA processing / mRNA cap binding complex binding / pi-body / P granule organization / piRNA binding / piRNA-mediated gene silencing by mRNA destabilization / transposable element silencing by piRNA-mediated heterochromatin formation / piRNA processing / sperm DNA condensation ...piP-body / primary piRNA processing / mRNA cap binding complex binding / pi-body / P granule organization / piRNA binding / piRNA-mediated gene silencing by mRNA destabilization / transposable element silencing by piRNA-mediated heterochromatin formation / piRNA processing / sperm DNA condensation / male meiotic nuclear division / chromatoid body / dense body / P granule / fertilization / regulatory ncRNA-mediated gene silencing / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / PIWI-interacting RNA (piRNA) biogenesis / spermatid development / RNA endonuclease activity / meiotic cell cycle / regulation of translation / spermatogenesis / single-stranded RNA binding / mRNA binding / protein kinase binding / mitochondrion / RNA binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
: / : / GAGE / GAGE protein / GAGE / : / : / Piwi, N-terminal domain / Tudor domain / Tudor domain profile. ...: / : / GAGE / GAGE protein / GAGE / : / : / Piwi, N-terminal domain / Tudor domain / Tudor domain profile. / Argonaute, linker 1 domain / Argonaute linker 1 domain / KH domain / Piwi domain profile. / Piwi domain / Piwi domain / Piwi / K Homology domain, type 1 / PAZ domain superfamily / PAZ / PAZ domain / Tudor domain / Tudor domain / PAZ domain profile. / PAZ domain / SNase-like, OB-fold superfamily / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Piwi-like protein 1 / Tudor and KH domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLiu, K. / Min, J.R. / Structural Genomics Consortium (SGC)
CitationJournal: Methods / Year: 2020
Title: Lesson from a Fab-enabled co-crystallization study of TDRD2 and PIWIL1.
Authors: Chen, S. / Zhang, W. / Min, J. / Liu, K.
History
DepositionJun 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 11, 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 / 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tudor and KH domain-containing protein
B: Uncharacterized protein
C: Fab antigen-binding fragment
D: Tudor and KH domain-containing protein
E: Uncharacterized protein
F: Fab antigen-binding fragment
G: Piwi-like protein 1


Theoretical massNumber of molelcules
Total (without water)153,61212
Polymers153,6127
Non-polymers05
Water00
1
A: Tudor and KH domain-containing protein
B: Uncharacterized protein
C: Fab antigen-binding fragment
G: Piwi-like protein 1


Theoretical massNumber of molelcules
Total (without water)77,6938
Polymers77,6934
Non-polymers04
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Tudor and KH domain-containing protein
E: Uncharacterized protein
F: Fab antigen-binding fragment


Theoretical massNumber of molelcules
Total (without water)75,9184
Polymers75,9183
Non-polymers01
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.099, 148.099, 168.026
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13C
23F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUPROPROAA306 - 4963 - 193
21GLUGLUPROPRODD306 - 4963 - 193
12ASPASPARGARGBB2 - 2122 - 212
22ASPASPARGARGEE2 - 2122 - 212
13GLUGLULYSLYSCC4 - 2284 - 228
23GLUGLULYSLYSFF4 - 2284 - 228

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Tudor and KH domain-containing protein / Tudor domain-containing protein 2


Mass: 24957.850 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TDRKH, TDRD2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y2W6
#2: Antibody Uncharacterized protein


Mass: 24612.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody Fab antigen-binding fragment


Mass: 26348.326 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Protein/peptide Piwi-like protein 1


Mass: 1774.991 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96J94*PLUS
#5: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 5 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: 3.46 Å3/Da / Density % sol: 64.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20.0% (V/V) PEG 3350, 0.2 M tri- lithium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.565
11-K, -H, -L20.435
ReflectionResolution: 2.8→48.48 Å / Num. obs: 51311 / % possible obs: 99.8 % / Redundancy: 11.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.033 / Rrim(I) all: 0.111 / Net I/σ(I): 16.6 / Num. measured all: 580022 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.8-2.8911.61.3165112844140.5650.4041.3771.8100
11.54-48.489.70.06166716870.9970.020.06532.889

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3pnw

3pnw


Resolution: 2.8→48.48 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.933 / SU B: 14.663 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.053
Details: The model was refined with refmac5 twin option and prosmart restraints derived from PDB entries 5ucb and 6b57.
RfactorNum. reflection% reflection
Rfree0.2062 2561 5 %
Rwork0.1904 --
obs0.1912 48719 99.83 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 165.78 Å2 / Biso mean: 79.148 Å2 / Biso min: 45.22 Å2
Baniso -1Baniso -2Baniso -3
1--18.85 Å2-0 Å2-0 Å2
2---18.85 Å2-0 Å2
3---37.69 Å2
Refinement stepCycle: final / Resolution: 2.8→48.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8993 0 5 0 8998
Biso mean--62.32 --
Num. residues----1251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0139239
X-RAY DIFFRACTIONr_bond_other_d0.0030.0177541
X-RAY DIFFRACTIONr_angle_refined_deg1.281.63712675
X-RAY DIFFRACTIONr_angle_other_deg1.1991.56817413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.94851241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.28922.663383
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.369151130
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3491533
X-RAY DIFFRACTIONr_chiral_restr0.040.21267
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210813
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021991
X-RAY DIFFRACTIONr_mcbond_it0.8053.5844988
X-RAY DIFFRACTIONr_mcbond_other0.8053.5844988
X-RAY DIFFRACTIONr_mcangle_it1.3655.3756221
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A53930.05
12D53930.05
21B49850.04
22E49850.04
31C60460.06
32F60460.06
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 175 -
Rwork0.254 3560 -
all-3735 -
obs--99.71 %
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)
15.73580.1905-1.06021.9998-0.32224.7802-0.04140.18430.1239-0.32010.07410.20070.0920.1535-0.03270.47440.0448-0.01950.3374-0.11060.0714-8.70468.32555.477
23.97170.42730.00992.14590.02211.5470.0053-0.4311-0.57810.2907-0.1233-0.17050.38070.12490.1180.42220.02460.02420.38030.04320.103-1.16770.92773.999
32.572-1.06590.17463.56961.32812.01-0.03380.4179-0.6426-0.4649-0.08050.30380.2936-0.20730.11430.4831-0.03930.00750.5689-0.18670.1892-15.16164.77650.491
46.4717-0.19842.85660.69241.11583.45260.12050.1185-0.3911-0.1845-0.01060.1787-0.23320.0523-0.10990.5581-0.01480.00120.51980.04940.7542-9.84916.56620.534
52.3962-0.67821.22192.7856-0.25253.14120.02680.5890.0625-0.6459-0.13590.1721-0.48470.07880.10910.8901-0.04730.00560.78010.07341.0804-2.26714.3472.426
61.94660.60770.04212.27680.03991.16020.0986-0.66050.2399-0.0072-0.03290.0936-0.4324-0.2502-0.06570.66690.01780.00590.80620.03591.0387-16.6219.325.65
71.35-2.5284-0.26585.44320.48881.9679-0.2254-0.1562-0.33520.58290.09930.08250.4478-0.1340.12610.6565-0.03680.1590.69520.16160.591218.94747.93470.426
83.5736-0.5969-0.31941.0745-0.11493.4064-0.0754-0.6907-0.28290.61640.2988-0.4568-0.01750.4522-0.22341.15260.1995-0.00410.96850.12071.14251.14933.40765.802
91.99480.09680.77073.4162-1.19681.2065-0.0520.7070.0558-0.68920.06030.44440.0778-0.2411-0.00830.6327-0.01430.07340.8896-0.01961.07416.65140.1995.564
103.23420.8461-0.57473.2218-0.12152.73360.19030.12660.3059-0.15350.07590.4224-0.180.053-0.26620.5407-0.03670.15790.4192-0.06080.175248.09755.2679.055
114.2444-2.5967-1.2382.46061.07621.38170.13370.1136-0.721-0.2687-0.20520.06270.11340.01660.07150.4948-0.0110.16480.3788-0.01860.3220.95257.01751.728
122.0939-2.57920.92263.4789-1.71342.3222-0.0512-0.322-0.4197-0.00570.28810.24710.60370.0531-0.23690.83330.05850.10020.77270.03491.027745.47830.70550.621
133.32650.47810.17780.7818-0.16430.48610.1948-0.057-0.033-0.0031-0.06080.35810.0446-0.1949-0.1340.5752-0.01160.09790.5052-0.04180.839919.15129.73324.195
143.86250.05541.25030.3961-0.97333.88710.073-0.01770.24910.10070.16620.2256-0.5811-0.0815-0.23920.6348-0.0640.26260.5171-0.06370.481642.7658.20124.755
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A306 - 326
2X-RAY DIFFRACTION2A327 - 417
3X-RAY DIFFRACTION3A418 - 497
4X-RAY DIFFRACTION4D306 - 326
5X-RAY DIFFRACTION5D327 - 417
6X-RAY DIFFRACTION6D418 - 497
7X-RAY DIFFRACTION7B2 - 108
8X-RAY DIFFRACTION8B109 - 212
9X-RAY DIFFRACTION9E2 - 108
10X-RAY DIFFRACTION10E109 - 212
11X-RAY DIFFRACTION11C4 - 126
12X-RAY DIFFRACTION12C127 - 228
13X-RAY DIFFRACTION13F4 - 126
14X-RAY DIFFRACTION14F127 - 228

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