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Project PXD019437

jPOSTrepo
replicated

Summary

Title

Crosslinking/mass spectrometry analysis of Bacillus subtilis RNAP-Delta-HelD complexes

Description

Crosslinking mass spectrometry was applied to investigate protein contacts and dramatic structural rearrangements triggered by HelD binding to RNAP. Four complexes RNAP螖未螖HelD , RNAP螖未螖HelD-未, RNAP螖未螖HelD-HelD and RNAP螖未螖HelD-未-HelD were assembled using RNAP purified from B. subtilis 螖helD螖ropE strain (RNAP螖未螖HelD), and recombinant 未 and HelD. The four complexes were crosslinked using a heterobifu...

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Sample Processing Protocol

We used crosslinking mass spectrometry to examine the effects of HelD binding to RNAP. We created four complexes using purified RNAP and recombinant 未 and HelD. We crosslinked the complexes using a photoactivatable crosslinker, then separated and analyzed them using LC-MS/MS and SEC.

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Data Processing Protocol

xiSEARCH and xiFDR software was used to analyzed the crosslinking peptides and proteins.

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Contact

Zhuo Chen , Technische Universit盲t Berlin

Juri Rappsilber , Technische Universit盲t Berlin (lab head)

Submission Date

27/05/2020

Publication Date

26/10/2020

Publication

DOI: 10.1038/s41467-020-20159-3, Des: Pei HH, Hilal T, Chen ZA, Huang YH, Gao Y, Said N, Loll B, Rappsilber J, Belogurov GA, Artsimovitch I, Wahl MC. The 未 subunit and NTPase HelD institute a two-pronged mechanism for RNA polymerase recycling. Nat Commun. 2020 11(1):6418

Visualizations

Name
Type
View
Bacillus-RNAP-Delta-HelD-S2-PlusSEC-PlusCopurified-SDA-Xi1-7-4-5LinkFDRBB-mzid
cross-linking
Bacillus-RNAP-Delta-S1-PlusSEC-PlusCopurified-SDA-Xi1-7-4-5LinkFDRBB-mzid
cross-linking
Bacillus-RNAP-HelD-S4-PlusSEC-PlusCopurified-SDA-Xi1-7-4-5LinkFDRBB-mzid
cross-linking
Bacillus-RNAP-S3-PlusSEC-PlusCopurified-SDA-Xi1-7-4-5LinkFDRBB-mzid
cross-linking

Project Files

Name
Type
Size (M)
Download
#
B200221_03_Lumos_ZC_CO_165_S3RNAP-SDA-10per.raw
RAW
994
a5dd9e66efb04135191e87b24739d7a0642acd466447150a934ec16db2a716c1
B200221_07_Lumos_ZC_CO_165_S1RNAP_Delta-SDA-10per.raw
RAW
962
7e6b95fa8b7f749f28f881ffd85d8ebf4a67a9713437a231cb736ebc1191a159
B200221_09_Lumos_ZC_CO_165_S4RNAP_HelD-SDA-10per.raw
RAW
1057
e638db27158e72d47adbeee18047f01f0168cda1443d59d8c23df06dedc53ce1
B200221_11_Lumos_ZC_CO_165_S2RNAP_Delta_HelD-SDA-10per.raw
RAW
977
bd94337f0010f6f810581f5700f0603363c9f8715f5fc31f92bd4dcdbf76ee20
B200304_02_Lumos_ZC_CO_140_xBacillusRNAP-S3-SDA-SECf5.raw
RAW
887
fa145f59e33675dcf0d7c93a8bbbbdb52b9059a62a72fa5a51178149265d4f52
B200304_03_Lumos_ZC_CO_140_xBacillusRNAP-S3-SDA-SECf6.raw
RAW
884
2187336223b99fa0feaca84cd4c6786c440e25f5d0c4581cda5a4e25cab51f45
B200304_04_Lumos_ZC_CO_140_xBacillusRNAP-S3-SDA-SECf7.raw
RAW
889
9de24c3be027d927d8d2f38b42722d1f4da04a7f86d6460dfc76c801979a169a
B200304_05_Lumos_ZC_CO_140_xBacillusRNAP-S3-SDA-SECf8.raw
RAW
849
f5f0f37b40dd20d30d7924b32ad96ed5c8c478e5ef16e823dd693f499099cdd7
B200304_06_Lumos_ZC_CO_140_xBacillusRNAP-S3-SDA-SECf9.raw
RAW
827
4e900c3467c16175d5a6504d20bb3b5b52fe2be53363be6004f348b8861b4f06
B200304_07_Lumos_ZC_CO_140_xBacillusRNAP-S3-SDA-SECf10.raw
RAW
779
7c753bce6c224dc25a08baaa89ed1f787c717324f0bce5f4dba2dc5913e48f58
B200306_02_Lumos_ZC_CO_140_xBacillusRNAP-S4-SDA-SECf5.raw
RAW
893
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B200306_03_Lumos_ZC_CO_140_xBacillusRNAP-S4-SDA-SECf6.raw
RAW
911
c355f10f7748423ed964a0cbf037228ff3917be8b265a40ceebe98eb25404aad
B200306_04_Lumos_ZC_CO_140_xBacillusRNAP-S4-SDA-SECf7.raw
RAW
900
908bd437c00cc68677cdaa25bddf695b4f3c4dc5240d361575ee3b2b60a0d72c
B200306_05_Lumos_ZC_CO_140_xBacillusRNAP-S4-SDA-SECf8.raw
RAW
869
b7f2a1616070ae9ecb0839acc522b78f0b6c5b9016ee304917db0546c9ba7784
B200306_06_Lumos_ZC_CO_140_xBacillusRNAP-S4-SDA-SECf9.raw
RAW
840
85545cb880af2f713a761bf1654c676dbb3bff4725dcbcbc8ba319858864768a
B200306_07_Lumos_ZC_CO_140_xBacillusRNAP-S4-SDA-SECf10.raw
RAW
809
91755f7b470ffa84e1ed53eace16ba150816b74226204dabe5eab29f3d99a5ec
B200306_10_Lumos_ZC_CO_140_xBacillusRNAP-S2-SDA-SECf5.raw
RAW
901
7ded0707f4b10c19b0f0599255869640a932ed0612d72101e8a6a44c4cec5aae
B200306_11_Lumos_ZC_CO_140_xBacillusRNAP-S2-SDA-SECf6.raw
RAW
910
a11dc3ab1eb4aa6627f89cb3facba3b47399745629c3b7ccc9e53b50dfc84d0f
B200306_12_Lumos_ZC_CO_140_xBacillusRNAP-S2-SDA-SECf7.raw
RAW
905
56f137b0e2c1143884051a2668c2c36074794fe515ecd2574f6a1dc4078cac93
B200306_13_Lumos_ZC_CO_140_xBacillusRNAP-S2-SDA-SECf8.raw
RAW
843
c74d6f889bfd58aa136030c9b52a80a62e02957caf293b0168c0aee44aed0687
    Total 61 items
  • 1
  • 2
  • 3
  • 4
    • 20 /page

Experimental Design (Samples)

Properties

Organism
Organism part

Unknown

Diseases

Unknown

Modification
Instrument
Software

Unknown

Experiment Type

Unknown

Quantification

Unknown

Dataset reuses

Not available

Number of files

RAW (28), SEARCH (0), PEAK (28), RESULT (4), OTHER (1)

License

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