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- PDB-3pnw: Crystal Structure of the tudor domain of human TDRD3 in complex w... -

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Basic information

Entry
Database: PDB / ID: 3pnw
TitleCrystal Structure of the tudor domain of human TDRD3 in complex with an anti-TDRD3 FAB
Components
  • FAB heavy chainFragment antigen-binding
  • FAB light chainFragment antigen-binding
  • Tudor domain-containing protein 3
KeywordsPROTEIN BINDING/IMMUNE SYSTEM / FAB / structural genomics consortium / antibody / SGC / PROTEIN BINDING-IMMUNE SYSTEM complex
Function / homology
Function and homology information


DNA topoisomerase III-beta-TDRD3 complex / DNA topological change / methylated histone binding / chromatin organization / transcription coactivator activity / chromatin binding / Golgi apparatus / RNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / Tudor domain-containing protein 3, UBA domain / RecQ mediated genome instability protein 1, N-terminal / RecQ mediated genome instability protein, N-terminal OB-fold superfamily / RMI1, N-terminal OB-fold domain / Tudor domain / Tudor domain profile. / UBA/TS-N domain / Tudor domain / Tudor domain ...: / Tudor domain-containing protein 3, UBA domain / RecQ mediated genome instability protein 1, N-terminal / RecQ mediated genome instability protein, N-terminal OB-fold superfamily / RMI1, N-terminal OB-fold domain / Tudor domain / Tudor domain profile. / UBA/TS-N domain / Tudor domain / Tudor domain / Ubiquitin associated domain / SH3 type barrels. - #140 / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / SH3 type barrels. / Roll / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tudor domain-containing protein 3
Similarity search - Component
Biological speciesHomo Sapiens (human)
synthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsLoppnau, P. / Tempel, W. / Wernimont, A.K. / Lam, R. / Ravichandran, M. / Adams-Cioaba, M.A. / Persson, H. / Sidhu, S.S. / Arrowsmith, C.H. / Edwards, A.M. ...Loppnau, P. / Tempel, W. / Wernimont, A.K. / Lam, R. / Ravichandran, M. / Adams-Cioaba, M.A. / Persson, H. / Sidhu, S.S. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Cossar, D. / Structural Genomics Consortium (SGC)
CitationJournal: J.Mol.Biol. / Year: 2013
Title: CDR-H3 Diversity Is Not Required for Antigen Recognition by Synthetic Antibodies.
Authors: Persson, H. / Ye, W. / Wernimont, A. / Adams, J.J. / Koide, A. / Koide, S. / Lam, R. / Sidhu, S.S.
History
DepositionNov 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 5, 2012Group: Database references
Revision 1.3Jan 9, 2013Group: Database references
Revision 1.4Feb 20, 2013Group: Database references
Revision 1.5Sep 18, 2013Group: Database references
Revision 1.6Sep 25, 2013Group: Source and taxonomy
Revision 1.7Nov 8, 2017Group: Refinement description / Category: software
Revision 1.8Sep 6, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FAB light chain
B: FAB heavy chain
C: Tudor domain-containing protein 3
D: FAB light chain
E: FAB heavy chain
F: Tudor domain-containing protein 3
G: FAB light chain
H: FAB heavy chain
I: Tudor domain-containing protein 3
J: FAB light chain
K: FAB heavy chain
L: Tudor domain-containing protein 3
M: FAB light chain
N: FAB heavy chain
O: Tudor domain-containing protein 3
P: FAB light chain
Q: FAB heavy chain
R: Tudor domain-containing protein 3
S: FAB light chain
T: FAB heavy chain
U: Tudor domain-containing protein 3
V: FAB light chain
W: FAB heavy chain
X: Tudor domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)480,294167
Polymers480,29424
Non-polymers0143
Water22,9691275
1
A: FAB light chain
B: FAB heavy chain
C: Tudor domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)60,03724
Polymers60,0373
Non-polymers021
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: FAB light chain
E: FAB heavy chain
F: Tudor domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)60,03720
Polymers60,0373
Non-polymers017
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: FAB light chain
H: FAB heavy chain
I: Tudor domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)60,03729
Polymers60,0373
Non-polymers026
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: FAB light chain
K: FAB heavy chain
L: Tudor domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)60,03716
Polymers60,0373
Non-polymers013
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
M: FAB light chain
N: FAB heavy chain
O: Tudor domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)60,03718
Polymers60,0373
Non-polymers015
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
P: FAB light chain
Q: FAB heavy chain
R: Tudor domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)60,03723
Polymers60,0373
Non-polymers020
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
S: FAB light chain
T: FAB heavy chain
U: Tudor domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)60,03717
Polymers60,0373
Non-polymers014
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
V: FAB light chain
W: FAB heavy chain
X: Tudor domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)60,03720
Polymers60,0373
Non-polymers017
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.708, 93.726, 159.932
Angle α, β, γ (deg.)80.960, 82.820, 90.060
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody
FAB light chain / Fragment antigen-binding


Mass: 24931.518 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo Sapiens, synthetic construct / Plasmid: pCW-FABV2HIS-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
#2: Antibody
FAB heavy chain / Fragment antigen-binding


Mass: 26130.115 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens, synthetic construct / Plasmid: pCW-FABV2HIS-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
#3: Protein
Tudor domain-containing protein 3


Mass: 8975.078 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TDRD3 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) codon plus RIL / References: UniProt: Q9H7E2
#4: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 143 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1275 / 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: 2.35 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 16% PEG-3350, 0.05M citric acid, 0.05M bis-tris propane, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 266201 / % possible obs: 97.4 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.086 / Χ2: 0.999 / Net I/σ(I): 6.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.05-2.122.30.414254570.966193.1
2.12-2.212.40.344261050.99195.7
2.21-2.312.40.299265441.011197
2.31-2.432.50.25266991.015197.6
2.43-2.582.50.193267091.021197.7
2.58-2.782.50.15267031.019197.9
2.78-3.062.60.112269531.026198.2
3.06-3.512.60.085269350.979198.6
3.51-4.422.60.065270021.004198.8
4.42-502.60.044270940.955199

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 2HFF (modified on FFAS03 server) and 3PMT

2hff

3pmt


Resolution: 2.05→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.285 / WRfactor Rwork: 0.234 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 15.604 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.218 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2635 2162 0.812 %thin shells (SFTOOLS)
Rwork0.2233 ---
obs0.224 266095 97.202 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso max: 150.63 Å2 / Biso mean: 45.03 Å2 / Biso min: 24.55 Å2
Baniso -1Baniso -2Baniso -3
1--1.951 Å2-0.248 Å20.076 Å2
2--0.537 Å2-2.489 Å2
3---2.177 Å2
Refinement stepCycle: LAST / Resolution: 2.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29516 0 143 1275 30934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02230607
X-RAY DIFFRACTIONr_bond_other_d0.0010.0219833
X-RAY DIFFRACTIONr_angle_refined_deg1.2671.9441855
X-RAY DIFFRACTIONr_angle_other_deg0.879348541
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.10153986
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.29424.0151173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.334154503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7491596
X-RAY DIFFRACTIONr_chiral_restr0.0780.24694
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02134555
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026285
X-RAY DIFFRACTIONr_mcbond_it0.761.519677
X-RAY DIFFRACTIONr_mcbond_other0.1751.57966
X-RAY DIFFRACTIONr_mcangle_it1.338231700
X-RAY DIFFRACTIONr_scbond_it2.03310930
X-RAY DIFFRACTIONr_scangle_it3.164.510115
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.10300.326182102015490.354
2.103-2.1600.307186771969694.826
2.16-2.2230.3033990.293180211911696.359
2.223-2.29100.283179831854496.975
2.291-2.36500.272175521800597.484
2.365-2.4480.3233860.261166421745297.57
2.448-2.5400.252164261680997.721
2.54-2.6420.2992960.25155831622697.861
2.642-2.75900.243152241555797.859
2.759-2.8920.2712660.236142321477198.152
2.892-3.04700.228139041414798.282
3.047-3.230.2642000.219129371334498.449
3.23-3.4500.205124261260098.619
3.45-3.7230.2451950.191113061165298.704
3.723-4.0720.2081250.185105561081698.752
4.072-4.54200.1639660975699.016
4.542-5.2240.2291300.1668427863399.12
5.224-6.3510.264840.27234736499.375
6.351-8.7860.356440.2215638571199.492
8.786-300.235370.2393295340297.942
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)
11.7135-0.05422.09190.4248-0.02643.71740.27770.2657-0.3136-0.0449-0.0455-0.00570.49610.1549-0.23210.20670.0312-0.01390.1803-0.07390.233520.7112-85.462625.4689
21.59880.1011.33040.39360.19311.6424-0.02960.071-0.12270.02390.00640.0930.0151-0.06880.02320.12170.01150.03150.11750.0060.082919.0732-69.885634.2371
35.1128-1.28081.76994.14741.04645.61460.261-0.3723-0.43950.49620.0581-0.26740.70460.3462-0.31910.32450.0244-0.1290.26450.10890.152641.3551-81.361166.362
41.52630.4334-1.34081.5337-1.19822.66440.14680.03280.30130.2127-0.09790.1402-0.3954-0.0265-0.04890.1864-0.02790.02460.16710.02170.440552.7396-25.648635.0219
51.91830.5887-0.92980.9081-0.61991.20830.0175-0.05420.30960.06930.0298-0.0876-0.0620.0547-0.04730.1355-0.0101-0.010.09070.01330.195454.972-42.928238.5963
68.9910.64080.19454.0736-1.039410.81750.1643-0.90470.44260.86480.13660.4843-0.2568-0.4888-0.30090.4863-0.0130.14910.5331-0.18560.364532.8315-42.217771.795
71.529-0.3070.73560.808-0.03692.81830.02940.3267-0.3365-0.0366-0.01430.04630.2080.0861-0.01510.1696-0.04660.04980.1774-0.08980.267158.9973-84.626325.4648
81.5218-0.1410.67690.48070.30041.8781-0.08260.091-0.13830.05570.00160.09090.0509-0.08970.08110.1455-0.04720.0280.1027-0.0010.099557.8435-68.569534.5565
95.5231-0.20920.31028.09671.9293.50750.2599-0.8666-0.59470.85430.0357-0.8570.5870.3513-0.29570.47170.0563-0.11260.5130.15850.214577.2304-82.035665.3309
100.98030.3574-0.63931.7479-1.43772.95030.00770.10650.27980.083-0.10650.0882-0.30130.0020.09880.14410.0073-0.02990.1614-0.0070.404215.0383-26.30535.0422
111.87740.3113-1.20081.0152-0.76442.1297-0.0499-0.0910.3090.00330.0018-0.1033-0.00210.18280.04810.11260.0075-0.03830.08180.00660.151515.9704-44.411939.0012
129.6694-0.2432-2.46918.1988-1.304910.40170.3281-1.06930.68061.39320.12941.0526-0.8044-0.5202-0.45750.49060.04590.29780.5774-0.1760.3769-3.3584-42.33772.1794
131.65910.2489-2.04640.5962-0.07384.30720.2305-0.31140.3185-0.0511-0.0248-0.0511-0.45880.3006-0.20570.2112-0.01190.0120.1932-0.08230.271759.03014.8896-34.8301
141.827-0.0125-1.26770.45520.38221.8093-0.001-0.09920.1586-0.08770.01060.0881-0.08180.0553-0.00960.14210.0367-0.03990.09560.01740.077157.208-10.6684-43.564
156.51751.4124-3.85723.92810.92446.06170.24390.53170.4679-0.90590.1449-0.4769-0.80840.2209-0.38880.5763-0.07470.17390.40430.06480.353379.80390.515-75.4867
161.38250.1848-1.01460.8205-0.03912.87420.0571-0.270.22870.0862-0.0230.0289-0.2347-0.0295-0.03410.14710.033-0.04720.1869-0.05670.183420.66314.0992-34.9049
171.34370.0918-0.98650.37360.15491.877-0.094-0.03610.0614-0.0142-0.0060.1191-0.0096-0.16170.09990.13840.0057-0.03650.1220.00740.072619.4479-12.0272-44.025
185.32431.7925-0.92895.03741.49485.34040.31930.5210.3686-0.77760.0614-0.5062-0.87030.4781-0.38070.3583-0.01250.09230.28920.07830.155639.26190.7932-75.9955
191.5933-0.771.40561.5905-1.52232.4740.1973-0.0454-0.2799-0.2163-0.14290.17870.39920.011-0.05450.18510.0205-0.03010.15490.0090.354914.5375-54.964-44.7712
201.8814-0.60971.13760.8068-0.56271.23520.00080.0722-0.2918-0.02010.054-0.0926-0.00640.144-0.05480.1174-0.01310.00710.10110.01520.155616.5452-37.5542-48.0271
219.142.12051.26158.29820.1769.32690.17111.191-0.6826-0.76920.18530.70880.3891-0.4342-0.35640.3450.0377-0.20930.4539-0.12220.2904-5.6661-38.3334-81.4471
221.27150.10120.46791.3844-1.18222.2605-0.0421-0.099-0.2747-0.1003-0.05470.02480.2229-0.07010.09680.17320.02690.01840.14660.01230.373853.5826-54.3088-44.5016
231.6621-0.16680.84610.9614-0.69881.6748-0.07160.0405-0.2833-0.0470.0449-0.0949-0.00170.0690.02670.12690.03030.01740.10170.01590.149454.5996-36.2847-48.1297
247.98633.94722.95216.22590.04817.71280.07751.1918-0.3784-1.19770.33961.22870.5155-0.6518-0.41710.5184-0.1225-0.27790.8383-0.00730.389235.6627-38.2592-81.8332
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999
5X-RAY DIFFRACTION5E-10 - 9999
6X-RAY DIFFRACTION6F-10 - 9999
7X-RAY DIFFRACTION7G-10 - 9999
8X-RAY DIFFRACTION8H-10 - 9999
9X-RAY DIFFRACTION9I-10 - 9999
10X-RAY DIFFRACTION10J-10 - 9999
11X-RAY DIFFRACTION11K-10 - 9999
12X-RAY DIFFRACTION12L-10 - 9999
13X-RAY DIFFRACTION13M-10 - 9999
14X-RAY DIFFRACTION14N-10 - 9999
15X-RAY DIFFRACTION15O-10 - 9999
16X-RAY DIFFRACTION16P-10 - 9999
17X-RAY DIFFRACTION17Q-10 - 9999
18X-RAY DIFFRACTION18R-10 - 9999
19X-RAY DIFFRACTION19S-10 - 9999
20X-RAY DIFFRACTION20T-10 - 9999
21X-RAY DIFFRACTION21U-10 - 9999
22X-RAY DIFFRACTION22V-10 - 9999
23X-RAY DIFFRACTION23W-10 - 9999
24X-RAY DIFFRACTION24X-10 - 9999

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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