Csu pilus rod type 1 stack

2026-04-01 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _citation_author.identifier_ORCID _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _citation_author.identifier_ORCID _em_admin.last_update DATABASE_REFERENCES citation citation_author em_admin _citation.journal_volume _citation_author.identifier_ORCID _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.journal_volume _citation_author.identifier_ORCID _em_admin.last_update PDBe PDBe 2025-01-23 2025-12-17 2025-12-17 2026-04-01 Academy of Finland 321762 Finland Academy of Finland 360760 Finland Sigrid Juselius Foundation 2023 Finland Csu pilus rod type 1 stack Malmi H Pakharukova N Zavialov AV pili, fimbriae, Acinetobacter baumannii pili, chaperone-usher pathway, archaic chaperone-usher pili, biofilm, 3D biofilm, adhesion, pathogenesis, pilus antiparallel binding junction, CELL ADHESION Malmi H Pakharukova N Paul B Tuittila M Ahmad I Knight SD Uhlin BE Ghosal D Zavialov AV Antiparallel stacking of Csu pili drives Acinetobacter baumannii 3D biofilm assembly. Nat Commun UK 17 2026 41654547 doi:10.1038/s41467-026-68860-z 2041-1723 9i3n FULLOVERLAP PDB 7ZL4 unspecified

The earlier structure depicts a single pilus rod, whereas the new structure depicts three pilus rods forming a stack.

PDB 9I37 unspecified

The other structure depicts a single pilus rod extracted from Acinetobacter baumannii, whereas this structure depicts three pilus rods forming a stack.

EMDB EMD-52601 associated EM volume

Csu pilus rod type 1 stack

Csu pilus rod type 1 stack Csu pilus rod type 1 stack 0 1

Csu pilus rods are homopolymers of subunit CsuA/B. The sample contains Csu pilus rods self-assembled into type 1 and type 2 stack architectures through antiparallel interactions. The stacks accumulate slowly over time as a gel-like substance at the bottom of a sample tube containing purified Csu pili.

Acinetobacter baumannii 19096 Planktonic bacteria Outer membrane Outer membrane 16.05974 CsuA/B Acinetobacter baumannii 19096 0.016069642

Csu pilus rods are homopolymers of subunit CsuA/B. Structure depicts three Csu pilus rods forming type 1 stack architecture through antiparallel interactions.

57 Escherichia coli BL21 LEVO AVTGQVDVKLNISTGCTVGGSQTEGNMNKFGTLNFGKTSGTWNNVLTAEVASAATGGNISVTCDGTDPVDFTVAIDGGER TDRTLKNTASADVVAYNVYRDAARTNLYVVNQPQQFTTVSGQATAVPIFGAIAPNTGTPKAQGDYKDTLLVTVNF A0A6F8TDQ5 singleParticle twoDArray 7.4 20.0 C8H18N2O4S HEPES 170.0 NaCl sodium chloride

Sample is a fraction taken from an ion exchange column elution gradient, so the NaCl concentration may vary.

Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY 20.0 GLOW DISCHARGE 20 AIR 0.014 ETHANE 100 277.15 FEI VITROBOT MARK IV

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 0.4 1.6 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 BIOQUANTUM (6k x 4k) 5760 4092 1 7941 2.79 59.848

Grid squares and holes were selected manually as the pilus stacks were visible in the atlas.

1 30605819

Two different types of Csu pilus stack architectures were solved from the same particle set. Particle picking failed to distinguish between the two, so the initial number of particles is the same for both stack architectures.

cryoSPARC v4.5.3 Patch CTF Correction PHASE FLIPPING AND AMPLITUDE CORRECTION

We used an earlier, unpublished 8.5 A map of Csu pilus type 1 stack as the starting model. It had been generated using Ab Initio reconstruction and another dataset.

7.58 FSC 0.143 CUT-OFF cryoSPARC v4.5.3 Local Refinement

Local Refinement allowed generating a single map without individual particles flipping and settling into pseudosymmetric orientations.

504940 MAXIMUM LIKELIHOOD cryoSPARC v4.5.3 Homogeneous Refinement and Heterogeneous Refinement

Homogeneous Refinement indicated that there are two types of stacks in the dataset. Generated masks based on an initial model overlapped with a 2D class allowed splitting the dataset between the two stack architectures.

MAXIMUM LIKELIHOOD cryoSPARC v4.5.3 8 cryoSPARC v4.5.3 Heterogeneous Refinement

The particles were too big for 3D Classification job, and the particles with Csu pilus stacks had a tendency to flip 180 degrees during refinement due to pseudosymmetries. We used models flipped 180 degrees in every direction as classes to collect the flipped particles and reorient them for local refinement. With the original model, six flipped models and one waste class, we had eight classes.

emd_52601.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 621 208 111 48 257 305 111 208 621 91.36743 171.21104 511.16373 90.0 90.0 90.0 Z Y X -0.13744208 0.31232294 0.002925161 0.06888288 0.82313 0.82313 0.82313 0.06 AUTHOR ::::EMDATABANK.org::::EMD-52601:::: Csu pilus type 1 antiparallel stack map, sharpened, pixel spacing adjusted, cropped around the model 7ZL4 24-178 PDB experimental model

The initial model consisted of a single pilus rod fragment of the same type. The initial model in turn is based on a crystal structure of CsuA/Bsc with PDB accession code 6FM5.

RIGID BODY FIT

UCSF Chimera was used to first fit the subunits into the single native pilus rod map (PDB Accession ID: 9I37) and average their relative angles, and it was also used to adjust pixel spacing of all maps to match model dimensions. Coot was used to adjust side chain and loop positions. A pair of antiparallel pili with subunit angles adjusted to 3-turns-per-7-subunits symmetry was overlapped with a 2D class to adjust the binding junction angle. Finally, Phenix was used to fit the type 1 stack model into the map.

REAL 668.100000000000023 emd_52601_msk_1.map emd_52601_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 720 720 720 0 0 0 720 720 720 592.6536 592.6536 592.6536 90.0 90.0 90.0 X Y Z -0.113228895 0.26640284 0.00005400999 0.01531014 0.82313 0.82313 0.82313 AUTHOR ::::EMDATABANK.org::::EMD-52601:::: Csu pilus type 1 antiparallel stack map, not sharpened, pixel spacing adjusted, not cropped around the model emd_52601_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 720 720 720 0 0 0 720 720 720 592.6536 592.6536 592.6536 90.0 90.0 90.0 X Y Z -0.13744208 0.31232294 0.000046508456 0.016765174 0.82313 0.82313 0.82313 AUTHOR ::::EMDATABANK.org::::EMD-52601:::: Csu pilus type 1 antiparallel stack map, sharpened, pixel spacing adjusted, not cropped around the model emd_52601_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 720 720 720 0 0 0 720 720 720 592.6536 592.6536 592.6536 90.0 90.0 90.0 X Y Z -1.3587024 1.4169768 0.00007307767 0.18081288 0.82313 0.82313 0.82313 AUTHOR ::::EMDATABANK.org::::EMD-52601:::: Csu pilus type 1 antiparallel stack map, half map A, pixel spacing adjusted emd_52601_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 720 720 720 0 0 0 720 720 720 592.6536 592.6536 592.6536 90.0 90.0 90.0 X Y Z -1.3888241 1.2992612 0.000065970766 0.17232701 0.82313 0.82313 0.82313 AUTHOR ::::EMDATABANK.org::::EMD-52601:::: Csu pilus type 1 antiparallel stack map, half map B, pixel spacing adjusted