Mechanisms of Opening and Closing of the Bacterial Replicative Helicase: The DnaB Helicase and Lambda P Helicase Loader Complex

2024-03-13 REL RCSB RCSB RCSB 2017-10-18 2019-03-06 2019-03-06 2024-03-13 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01 GM084162 United States National Science Foundation (NSF, United States) MCB 1818255 United States National Institutes of Health/National Institute on Minority Health and Health Disparities (NIH/NIMHD) 5G12MD007603-30 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) P41 GM109824 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) P41 GM103314 United States Other government PA200A150068 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) F32GM128303 United States Other private SF349247 (Simons Foundation) United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM103310 United States Other private F00316 (Agouron Institute) United States National Institutes of Health/Office of the Director OD019994 United States Other private SM-2015-289297 (Silicon Mechanics/Research Cluster Grant program) United States Mechanisms of Opening and Closing of the Bacterial Replicative Helicase: The DnaB Helicase and Lambda P Helicase Loader Complex Chase J Catalano A Helicase Loader, Helicase, DNA replication, ATPase, DNA Replication Initiation, Bacteriophage Lambda, REPLICATION Chase J Catalano A Noble AJ Eng ET Olinares PD Molloy K Pakotiprapha D Samuels M Chait B des Georges A Jeruzalmi D Mechanisms of opening and closing of the bacterial replicative helicase. Elife US 7 2018 30582519 doi:10.7554/eLife.41140 2050-084X 6bbm FULLOVERLAP DnaB helicase - Lambda P helicase loader DNA replication complex DnaB helicase - Lambda P helicase loader DNA replication complex 0 1 2

pET24a containing full-length DnaB was co-expressed with pCDFDuet containing full-length LambdaP in BL21(DE3) cells. The resolution of the LambdaP portion of our EM map did not permit the unambiguous assignment of the amino acid sequence to the structure. As such, the model for LambdaP was built as a poly alanine model. Additionally, only half of LambdaP was observed in our maps due to the intrinsic flexibility of the amino and carboxy terminal domains of LambdaP. Subsequent experiments determined that the observed portion of LambdaP in our maps corresponds to the C-terminal domain.

Escherichia coli E coli DnaB helicase 1 1

E coli DnaB helicase is observed as an open-spiral hexamer, in which one of the interfaces is breached. Five ADP molecules are observed at the five intact ATP binding sites. Additionally, clear density is observed for five of six linkers permitting unambiguous assignment of NTD to parent CTD domain.

Escherichia coli Lambda P helicase loader 1 2

Five lambda P molecules were observed bound to the five intact DnaB subunit interfaces. Unambiguous assignment of side chain density for lambda P was not possible due to the resolution of this region of the EM map. Instead, a polyalanine model was built for each lambda P molecule. Additionally, density for approximately half of the expected 233 residues of lambda P was observed owing to flexibility between domains. Subsequent experiments confirmed that the observed region of Lambda P is the C-terminal domain, which interacts with DnaB.

Enterobacteria phage lambda Replicative DNA helicase Escherichia coli O111:NM 0.052450945 6 Escherichia coli BL21(DE3) LEVO MAGNKPFNKQQAEPRERDPQVAGLKVPPHSIEAEQSVLGGLMLDNERWDDVAERVVADDFYTRPHRHIFTEMARLQESGS PIDLITLAESLERQGQLDSVGGFAYLAELSKNTPSAANISAYADIVRERAVVREMISVANEIAEAGFDPQGRTSEDLLDL AESRVFKIAESRANKDEGPKNIADVLDATVARIEQLFQQPHDGVTGVNTGYDDLNKKTAGLQPSDLIIVAARPSMGKTTF AMNLVENAAMLQDKPVLIFSLEMPSEQIMMRSLASLSRVDQTKIRTGQLDDEDWARISGTMGILLEKRNIYIDDSSGLTP TEVRSRARRIAREHGGIGLIMIDYLQLMRVPALSDNRTLEIAEISRSLKALAKELNVPVVALSQLNRSLEQRADKRPVNS DLRESGSIEQDADLIMFIYRDEVYHENSDLKGIAEIIIGKQRNGPIGTVRLTFNGQWSRFDNYAGPQYDDE A0A365Q7M1 3.6.4.12 Replication protein P Escherichia phage lambda 0.023141221 5 Escherichia coli BL21(DE3) LEVO MKNIAAQMVNFDREQMRRIANNMPEQYDEKPQVQQVAQIINGVFSQLLATFPASLANRDQNEVNEIRRQWVLAFRENGIT TMEQVNAGMRVARRQNRPFLPSPGQFV(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) P03689 ADENOSINE-5'-DIPHOSPHATE 0.000427201 5 ADP singleParticle particle 0.48 7.5 20.0 Na-HEPES Sodium HEPES 450.0 NaCl Sodium Chloride 2.0 DTT Dithiothreitol 0.5 MgCl2 Magnesium Chloride 0.5 ATP Adenosine triphosphate

Concentrated BP sample (18mg/mL) was diluted with freshly prepared buffer to desired concentration (~1.5 micromolar) for grid preparation.

Quantifoil R0.6/1 GOLD 400 CARBON CONTINUOUS PLASMA CLEANING 60 OTHER

The grid was coated with 50 nm of evaporated gold prior to use. All remaining carbon was removed by plasma cleaning for 5 minutes in a Gatan Solarus plasma cleaner.

ETHANE 100 277.15 FEI VITROBOT MARK IV

3uL of sample was adhered to a fresh plasma cleaned grid and allowed to adsorb for 30 seconds, blotted for 3 seconds with a blot force of 4 and plunge frozen into liquid nitrogen-cooled ethane..

The sample was monodisperse. Side views were more electron weak than top or bottom views creating challenges for particle picking. This issue was overcome with cryo-electron tomography techniques used for 1) initial model generation and 2) template generation for particle picking.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 -0.001 -0.003 22500.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 70.0 70.0 The Krios this data was collected on has a Cs of 2.7.

Preliminary grid screening was performed prior to Krios data collections. All microscope alignments were completed by the New York Structural Biology SEMC team.

GATAN K2 SUMMIT (4k x 4k) COUNTING 3838 3710 1-50 3 2426 10.0 8.0

Single particle movies were recorded at a pixel size of 1.07 angstroms/pixel. Three 24-hour sessions produced 2,426 micrograph movies. In addition, five tilt series were collected from the same grids bi-directionally over a tilt range of -45 degrees to +45 degrees in 3 degree increments at a dose of 2.57 to 3.3 electrons per angstrom squared (total accumulated dose of 90 electrons per angstrom squared). Tilt series were collected at a pixel size of 1.76 angstroms and at defocus values of -2.8um, -6.1um and -9.3um.

Images collected were CTF corrected and selected based on CTF estimates of less than 10 angstrom at a confidence cutoff of 0.8 for subsequent processing.

1000 -45 45

Three tilt series were collected from same single-particle grids at a pixel size of 1.76 angstroms per pixel and defocus values of -2.8um, -6.1um and -9.3um. Tilt series were collected bi-directionally over a tilt range of -45 degrees to +45 degrees in 3 degree increments, with a dose of 2.57 to 3.3 electrons per angstrom squared per tilt increment (subdivided over seven to nine frames.) A low resolution initial model was generated from ~1,000 particles picked from three tilt series. These tilt series were first aligned using a fiducial-less algorithm implemented in Appion-Portomo, then reconstructed using Tomo3D. 1,000 particles were picked from resulting tomograms (binned 4 x 4) to generate a ~40 angstrom initial model. Resolution was estimated by filtering procedures. The resulting volume served as an initial model and was projected to generate templates for template-based particle picking of single particle micrographs.

4.1 FSC 0.143 CUT-OFF RELION Auto refine and post processing was performed in Relion. Dynamo Dynamo was used to generate sub-tomogram average, later used as initial model.

Relion was used to independently refine half sets using 0.143 gold-standard to a resolution of 4.1A. A total of 90,883 particles went into this reconstruction.

90883 emd_7076.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 273.92 273.92 273.92 90.0 90.0 90.0 X Y Z -0.09008105 0.161977 0.000051110845 0.0061288467 1.07 1.07 1.07 0.0276 AUTHOR ::::EMDATABANK.org::::EMD-7076:::: DnaB-LambdaP helicase-helicase loader complex from single particle cryoEM at 4.1A. The suggested viewing thresholds are 0.0276 (Chimera) or an isomesh level of 6 (PyMol). 2R5U 1-173 PDB experimental model 3BH0 203-441 PDB experimental model FLEXIBLE FIT

The initial fitting was done with the 2R5U and 3BH0 models onto which the E. coli amino sequence had been built. The linker segments that connected these segments were built by hand. PHENIX real_space_refine was used to refine the complete model for the B6P5 entity.

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