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- PDB-8dn6: The crystal structure of the Arabidopsis thaliana Toc75 POTRA dom... -

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Basic information

Entry
Database: PDB / ID: 8dn6
TitleThe crystal structure of the Arabidopsis thaliana Toc75 POTRA domains in complex with fab tc2
Components
  • Protein TOC75-3, chloroplastic
  • fabtc2_HC
  • fabtc2_LC
KeywordsMEMBRANE PROTEIN / Chloroplast / Fabs
Function / homology
Function and homology information


Toc complex / TOC-TIC supercomplex I / protein targeting to chloroplast / protein import into chloroplast stroma / chloroplast organization / protein-transporting ATPase activity / embryonic morphogenesis / chloroplast envelope / plant-type vacuole / plastid ...Toc complex / TOC-TIC supercomplex I / protein targeting to chloroplast / protein import into chloroplast stroma / chloroplast organization / protein-transporting ATPase activity / embryonic morphogenesis / chloroplast envelope / plant-type vacuole / plastid / chloroplast / intracellular protein transport / cytosol
Similarity search - Function
Chloroplast envelope protein translocase, IAP75 / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain
Similarity search - Domain/homology
Protein TOC75-3, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsSrinivasan, K. / Noinaj, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM127896-01 United States
CitationJournal: Structure / Year: 2023
Title: Characterization of synthetic antigen binding fragments targeting Toc75 for the isolation of TOC in A. thaliana and P. sativum.
Authors: Srinivasan, K. / Erramilli, S.K. / Chakravarthy, S. / Gonzalez, A. / Kossiakoff, A. / Noinaj, N.
History
DepositionJul 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein TOC75-3, chloroplastic
B: Protein TOC75-3, chloroplastic
C: fabtc2_HC
D: fabtc2_LC
E: fabtc2_HC
F: fabtc2_LC


Theoretical massNumber of molelcules
Total (without water)169,7336
Polymers169,7336
Non-polymers00
Water00
1
A: Protein TOC75-3, chloroplastic
C: fabtc2_HC
D: fabtc2_LC


Theoretical massNumber of molelcules
Total (without water)84,8663
Polymers84,8663
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-39 kcal/mol
Surface area28700 Å2
MethodPISA
2
B: Protein TOC75-3, chloroplastic
E: fabtc2_HC
F: fabtc2_LC


Theoretical massNumber of molelcules
Total (without water)84,8663
Polymers84,8663
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-33 kcal/mol
Surface area28850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)276.089, 51.481, 172.082
Angle α, β, γ (deg.)90.000, 123.060, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 252 through 261 or (resid 262...
21(chain B and (resid 252 through 253 or (resid 254...
12(chain C and (resid 4 through 19 or resid 21...
22(chain E and (resid 4 through 5 or (resid 6...
13(chain D and (resid 2 through 149 or (resid 150...
23(chain F and (resid 2 through 156 or resid 158 through 215))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPLEULEU(chain A and (resid 252 through 261 or (resid 262...AA252 - 261116 - 125
121METMETMETMET(chain A and (resid 252 through 261 or (resid 262...AA262126
131ASPASPGLUGLU(chain A and (resid 252 through 261 or (resid 262...AA252 - 449116 - 313
141ASPASPGLUGLU(chain A and (resid 252 through 261 or (resid 262...AA252 - 449116 - 313
151ASPASPGLUGLU(chain A and (resid 252 through 261 or (resid 262...AA252 - 449116 - 313
161ASPASPGLUGLU(chain A and (resid 252 through 261 or (resid 262...AA252 - 449116 - 313
211ASPASPARGARG(chain B and (resid 252 through 253 or (resid 254...BB252 - 253116 - 117
221PHEPHEPHEPHE(chain B and (resid 252 through 253 or (resid 254...BB254118
231ASPASPGLUGLU(chain B and (resid 252 through 253 or (resid 254...BB252 - 449116 - 313
241ASPASPGLUGLU(chain B and (resid 252 through 253 or (resid 254...BB252 - 449116 - 313
251ASPASPGLUGLU(chain B and (resid 252 through 253 or (resid 254...BB252 - 449116 - 313
261ASPASPGLUGLU(chain B and (resid 252 through 253 or (resid 254...BB252 - 449116 - 313
112GLUGLUGLYGLY(chain C and (resid 4 through 19 or resid 21...CC4 - 194 - 19
122LEULEULEULEU(chain C and (resid 4 through 19 or resid 21...CC21 - 8921 - 89
132SERSERLYSLYS(chain C and (resid 4 through 19 or resid 21...CC3 - 2243 - 224
142SERSERLYSLYS(chain C and (resid 4 through 19 or resid 21...CC3 - 2243 - 224
152SERSERLYSLYS(chain C and (resid 4 through 19 or resid 21...CC3 - 2243 - 224
162SERSERLYSLYS(chain C and (resid 4 through 19 or resid 21...CC3 - 2243 - 224
172SERSERLYSLYS(chain C and (resid 4 through 19 or resid 21...CC3 - 2243 - 224
182SERSERLYSLYS(chain C and (resid 4 through 19 or resid 21...CC3 - 2243 - 224
212GLUGLUVALVAL(chain E and (resid 4 through 5 or (resid 6...EE4 - 54 - 5
222GLNGLNGLNGLN(chain E and (resid 4 through 5 or (resid 6...EE66
232GLUGLUPROPRO(chain E and (resid 4 through 5 or (resid 6...EE4 - 2234 - 223
242GLUGLUPROPRO(chain E and (resid 4 through 5 or (resid 6...EE4 - 2234 - 223
252GLUGLUPROPRO(chain E and (resid 4 through 5 or (resid 6...EE4 - 2234 - 223
262GLUGLUPROPRO(chain E and (resid 4 through 5 or (resid 6...EE4 - 2234 - 223
113ASPASPTRPTRP(chain D and (resid 2 through 149 or (resid 150...DD2 - 1492 - 149
123LYSLYSLYSLYS(chain D and (resid 2 through 149 or (resid 150...DD150150
133ASPASPCYSCYS(chain D and (resid 2 through 149 or (resid 150...DD2 - 2152 - 215
143ASPASPCYSCYS(chain D and (resid 2 through 149 or (resid 150...DD2 - 2152 - 215
153ASPASPCYSCYS(chain D and (resid 2 through 149 or (resid 150...DD2 - 2152 - 215
163ASPASPCYSCYS(chain D and (resid 2 through 149 or (resid 150...DD2 - 2152 - 215
213ASPASPGLNGLN(chain F and (resid 2 through 156 or resid 158 through 215))FF2 - 1562 - 156
223GLYGLYCYSCYS(chain F and (resid 2 through 156 or resid 158 through 215))FF158 - 215158 - 215

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Protein TOC75-3, chloroplastic / 75 kDa translocon at the outer-envelope-membrane of chloroplasts 3 / AtTOC75-III


Mass: 35628.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TOC75-3, TOC75, At3g46740, T6H20.230 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9STE8
#2: Antibody fabtc2_HC


Mass: 25726.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Antibody fabtc2_LC


Mass: 23511.119 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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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: 3.02 Å3/Da / Density % sol: 59.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 16% PEG 4000, 20% Glycerol, 0.1M Sodium Citrate pH 5.8, 0.1M Ammonium Sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 41871 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 59.81 Å2 / CC1/2: 0.982 / CC star: 0.995 / Rpim(I) all: 0.138 / Rrim(I) all: 0.347 / Net I/σ(I): 7.28
Reflection shellResolution: 3→3.11 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 1.21 / Num. unique obs: 4117 / CC1/2: 0.37 / CC star: 0.735 / Rpim(I) all: 0.682 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.20_4459refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BJZ, 5UAY

5bjz

5uay


Resolution: 3→49.3 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.293 1990 4.78 %
Rwork0.2397 39659 -
obs0.2423 41649 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 223.34 Å2 / Biso mean: 77.7576 Å2 / Biso min: 10.43 Å2
Refinement stepCycle: final / Resolution: 3→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9633 0 0 0 9633
Num. residues----1267
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1769X-RAY DIFFRACTION18.641TORSIONAL
12B1769X-RAY DIFFRACTION18.641TORSIONAL
21C1810X-RAY DIFFRACTION18.641TORSIONAL
22E1810X-RAY DIFFRACTION18.641TORSIONAL
31D1841X-RAY DIFFRACTION18.641TORSIONAL
32F1841X-RAY DIFFRACTION18.641TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3-3.060.43081290.3822260792
3.06-3.140.42421390.362279699
3.14-3.230.42561410.341281499
3.23-3.340.35491410.3194281199
3.34-3.460.32581430.28342845100
3.46-3.60.34051420.2604281699
3.6-3.760.36461400.2735281099
3.76-3.960.33051440.2744284099
3.96-4.210.31411430.23392827100
4.21-4.530.2451430.19222853100
4.53-4.990.21061450.18162864100
4.99-5.710.24721430.1878288899
5.71-7.180.27071470.22632896100
7.19-49.30.22751500.1901299299
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)
10.08580.1174-0.02540.0891-0.07110.1188-0.00430.0402-0.05140.34260.1350.13130.260.17420.10630.8433-0.024-0.00640.1591-0.01030.456126.7901-30.8718-12.2451
20.23540.1007-0.13850.8191-0.20451.0199-0.06640.04180.15880.07860.38810.10760.05240.06110.55710.21010.02950.07020.2049-0.17950.187324.8573-11.4623-25.3499
30.1993-0.1141-0.1060.23240.10480.2577-0.14360.18150.14670.1270.17870.30840.1642-0.01760.15610.3048-0.0440.00910.34120.14790.41547.6109-4.8876-35.5117
40.08020.0084-0.04630.1686-0.06420.0467-0.08590.01260.1452-0.21420.15140.02390.0466-0.06940.10180.4246-0.05470.03310.0299-0.05990.384561.3118-28.20383.7469
50.005-0.0148-0.00870.0293-0.08490.0335-0.1239-0.07480.15310.40610.0488-0.01050.3033-0.0941-0.0510.1711-0.26740.1192-0.65570.6009-0.290955.3136-20.474788.8306
60.0706-0.0663-0.11040.12760.09730.10720.0294-0.15550.115-0.06970.2871-0.20040.11820.08590.24510.2498-0.34130.0293-0.08510.15220.288572.684-10.729795.4767
70.20810.0212-0.03750.24960.120.21170.0096-0.0223-0.0881-0.10370.0637-0.04380.22510.21770.28930.31550.05370.07210.1376-0.13440.422279.2803-5.2721104.5616
80.2782-0.07290.01890.3381-0.03540.00130.09360.1069-0.0033-0.1065-0.288-0.06760.38980.3642-0.27480.47570.4316-0.08080.7577-0.16810.342442.3685-20.06464.6715
90.26970.0340.15870.4894-0.22760.2103-0.1172-0.33010.158-0.2834-0.10.23080.050.3457-0.24310.25920.113-0.08670.7968-0.0560.384137.5705-13.524115.3285
100.0441-0.19870.07881.6702-0.44240.14350.008-0.0648-0.10080.47510.20910.06580.02160.35750.11750.2985-0.1238-0.05410.7095-0.09850.354229.8429-4.861837.1596
110.0802-0.18850.16390.5656-0.39690.3551-0.0940.0543-0.07040.0281-0.1478-0.12120.1869-0.11-0.26510.49290.0207-0.04420.4055-0.25440.47217.229-9.27254.3713
120.01020.0395-0.01720.0338-0.016-0.00250.1176-0.22010.2458-0.0534-0.23830.02630.1363-0.102400.49930.031-0.06780.39540.04930.44121.6691-18.93631.5098
130.00280.00270.00110.00610.00410.0044-0.00870.0728-0.0688-0.1583-0.0968-0.017-0.0466-0.01550.00010.60740.1294-0.05730.6017-0.06550.311315.8643-15.8218-3.5512
140.00230.0070.00470.00260.00350.0050.07260.01580.04760.0289-0.1323-0.23110.2090.07640.00030.43290.00910.00590.703-0.17930.332919.6658-16.88456.4445
150.0104-0.00610.0145-0.0062-0.00350.01650.1125-0.2310.0683-0.1401-0.03420.16230.1065-0.17130.00010.53250.0283-0.00840.8125-0.2080.365126.582-11.81543.0315
160.0245-0.0278-0.03980.08240.01710.0903-0.05310.0408-0.1354-0.0901-0.09320.0166-0.0423-0.085-0.07250.4712-0.18790.05920.4369-0.28220.438516.33763.124229.9011
170.086-0.0402-0.02350.02570.02980.1062-0.1188-0.01680.02280.19130.012-0.03270.0067-0.0939-0.07710.3045-0.13-0.09180.6038-0.31450.521331.27617.729335.4557
180.01330.0107-0.01690.02190.00240.03450.1077-0.00960.0469-0.1103-0.0066-0.0115-0.1030.09960.03090.4481-0.06510.02680.2549-0.14790.488618.75626.157222.7364
190.0017-0.00260.00370.0055-0.00290.00450.17540.07350.064-0.01220.11260.0123-0.0964-0.00260.0460.4845-0.22030.06160.4025-0.04780.62828.177512.089123.5376
200.00350.0030.00120.0033-0.00190.0023-0.036-0.0356-0.04960.08440.0449-0.10050.0217-0.0248-00.66150.00930.14390.558-0.18410.624215.8545-7.929425.0817
210.03580.0177-0.02710.016-0.01870.0343-0.0131-0.04930.0367-0.1270.07690.09590.02950.00340.00040.3909-0.16380.03220.3041-0.13030.64928.02713.885130.0556
220.0088-0.0056-0.00640.00780.0110.0018-0.00060.00440.1329-0.03290.098-0.0397-0.0541-0.06800.7561-0.0036-0.0210.6757-0.25140.822918.087214.302732.437
230.2059-0.07880.09460.2262-0.01330.0423-0.03330.20270.1457-0.0309-0.0929-0.00870.1562-0.3169-0.13340.4687-0.23340.01350.44920.01220.363249.3189-21.295462.1655
240.1546-0.147-0.12470.13390.13880.07590.14960.3421-0.0423-0.0549-0.3326-0.04990.162-0.372-0.02090.3309-0.1861-0.05840.6233-0.04420.394849.4837-17.157459.3581
250.6926-0.0764-0.27740.14560.0440.1599-0.08410.5806-0.1906-0.13510.1152-0.1212-0.29530.1437-0.03190.32820.04970.00740.81930.08920.29667.8262-2.66932.7018
260.03250.03080.07890.06420.07870.19990.21150.081-0.0590.22530.0082-0.2918-0.03880.30690.02020.3947-0.0696-0.03250.28760.0990.529470.7352-10.721271.4421
270.2491-0.0730.19750.0746-0.10830.20210.20120.08950.29050.1117-0.09740.02240.21930.01760.02460.3932-0.009-0.0270.16430.0080.301570.6662-20.199267.5188
280.14870.084-0.02620.03440.00410.01280.07140.07970.03860.1609-0.2457-0.05430.13220.007-0.00240.55640.05410.01110.70010.17830.34364.0862-12.520666.9908
290.07050.0723-0.02410.09390.00360.0430.1125-0.08720.01660.03640.0179-0.06620.01810.06620.2160.2284-0.0146-0.05740.55470.44930.607978.89333.174943.1841
300.03780.0241-0.07260.14620.03540.16580.19160.06110.0723-0.06420.20760.1846-0.0764-0.18940.26120.52010.11070.02790.44230.28960.549370.31996.874843.0453
310.0601-0.01610.03950.0334-0.01080.056-0.1798-0.0375-0.00060.35640.0609-0.1992-0.1925-0.2755-0.00240.25850.03050.06670.27560.03770.331371.59810.051844.1271
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 252 through 296 )A252 - 296
2X-RAY DIFFRACTION2chain 'A' and (resid 297 through 386 )A297 - 386
3X-RAY DIFFRACTION3chain 'A' and (resid 387 through 449 )A387 - 449
4X-RAY DIFFRACTION4chain 'B' and (resid 252 through 276 )B252 - 276
5X-RAY DIFFRACTION5chain 'B' and (resid 277 through 338 )B277 - 338
6X-RAY DIFFRACTION6chain 'B' and (resid 339 through 386 )B339 - 386
7X-RAY DIFFRACTION7chain 'B' and (resid 387 through 449 )B387 - 449
8X-RAY DIFFRACTION8chain 'C' and (resid 3 through 76 )C3 - 76
9X-RAY DIFFRACTION9chain 'C' and (resid 77 through 144 )C77 - 144
10X-RAY DIFFRACTION10chain 'C' and (resid 145 through 224 )C145 - 224
11X-RAY DIFFRACTION11chain 'D' and (resid 2 through 19 )D2 - 19
12X-RAY DIFFRACTION12chain 'D' and (resid 20 through 62 )D20 - 62
13X-RAY DIFFRACTION13chain 'D' and (resid 63 through 76 )D63 - 76
14X-RAY DIFFRACTION14chain 'D' and (resid 77 through 93 )D77 - 93
15X-RAY DIFFRACTION15chain 'D' and (resid 94 through 107 )D94 - 107
16X-RAY DIFFRACTION16chain 'D' and (resid 108 through 122 )D108 - 122
17X-RAY DIFFRACTION17chain 'D' and (resid 123 through 138 )D123 - 138
18X-RAY DIFFRACTION18chain 'D' and (resid 139 through 151 )D139 - 151
19X-RAY DIFFRACTION19chain 'D' and (resid 152 through 164 )D152 - 164
20X-RAY DIFFRACTION20chain 'D' and (resid 165 through 175 )D165 - 175
21X-RAY DIFFRACTION21chain 'D' and (resid 176 through 199 )D176 - 199
22X-RAY DIFFRACTION22chain 'D' and (resid 200 through 215 )D200 - 215
23X-RAY DIFFRACTION23chain 'E' and (resid 4 through 63 )E4 - 63
24X-RAY DIFFRACTION24chain 'E' and (resid 64 through 130 )E64 - 130
25X-RAY DIFFRACTION25chain 'E' and (resid 131 through 223 )E131 - 223
26X-RAY DIFFRACTION26chain 'F' and (resid 1 through 33 )F1 - 33
27X-RAY DIFFRACTION27chain 'F' and (resid 34 through 93 )F34 - 93
28X-RAY DIFFRACTION28chain 'F' and (resid 94 through 107 )F94 - 107
29X-RAY DIFFRACTION29chain 'F' and (resid 108 through 122 )F108 - 122
30X-RAY DIFFRACTION30chain 'F' and (resid 123 through 151 )F123 - 151
31X-RAY DIFFRACTION31chain 'F' and (resid 152 through 215 )F152 - 215

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • 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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