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 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.page_first _citation.page_last _citation.year _citation_author.identifier_ORCID _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation_author.identifier_ORCID _em_admin.last_update PDBe PDBe 2025-03-31 2025-06-18 2025-06-18 2026-04-01 Biotechnology and Biological Sciences Research Council (BBSRC) BB/W009986/1 United Kingdom Biotechnology and Biological Sciences Research Council (BBSRC) BB/X01102X/1 United Kingdom Wellcome Trust 221868/Z/20/Z United Kingdom Biotechnology and Biological Sciences Research Council (BBSRC) BB/X01097X/1 United Kingdom Department of Energy (DOE, United States) DE-SC0018143 United States Biotechnology and Biological Sciences Research Council (BBSRC) BBS/E/J/000PR9797 United Kingdom Royal Society ICA/R1/180088 United Kingdom Biotechnology and Biological Sciences Research Council (BBSRC) BB/CCG2240/1 United Kingdom Wellcome Trust 218785/Z/19/Z United Kingdom Structure of the Azotobacter vinelandii NifL-NifA complex Bueno Batista M Richardson J Webster MW Ghilarov D Peters JW Lawson DM Dixon R biological nitrogen fixation, transcriptional regulation, sustainable agriculture, GENE REGULATION Bueno Batista M Richardson J Webster MW Ghilarov D Peters JW Lawson DM Dixon R Structural analysis of the NifL-NifA complex reveals the molecular basis of anti-activation of nitrogen fixation gene expression in Azotobacter vinelandii. Febs J. UK 293 1643 1663 2026 40915976 doi:10.1111/febs.70253 1742-464X 9qq6 FULLOVERLAP EMDB EMD-53294 associated EM volume
Structure of the Azotobacter vinelandii NifL-NifA complex
 NifL-NifA complex from Azotobacter vinelandii NifL-NifA complex from Azotobacter vinelandii 0 1 2 Azotobacter vinelandii DJ 0.24 histidine kinase Azotobacter vinelandii DJ 0.059897202999999996
The wild-type sequence was pre-pended by a Strep-Tag II in place of the N-terminal methionine with sequence MASWSHPQFEKGADDDDKV
2 Escherichia coli BL21(DE3) LEVO MASWSHPQFEKGADDDDKVTPANPTLSNEPQAPHAESDELLPEIFRQTVEHAPIAISITDLKANILYANRAFRTITGYGS EEVLGKNESILSNGTTPRLVYQALWGRLAQKKPWSGVLVNRRKDKTLYLAELTVAPVLNEAGETIYYLGMHRDTSELHEL EQRVNNQRLMIEAVVNAAPAAMVVLDRQHRVMLSNPSFCRLARDLVEDGSSESLVALLRENLAAPFETLENQGSAFSGKE ISFDLGGRSPRWLSCHGRAIHIENEQAHVFFAPTEERYLLLTINDISELRQKQQDSRLNALKALMAEEELLEGMRETFNA AIHRLQGPVNLISAAMRMLERRLGDKAGNDPVLSAMREASTAGMEALENLSGSIPVRMAESKMPVNLNQLIREVITLCTD QLLAQGIVVDWQPALRLPWVMGGESSLRSMIKHLVDNAIESMSQNQVSRRELFISTRVENHLVRMEITDSGPGIPPDLVL KVFEPFFSTKPPHRVGRGMGLPVVQEIVAKHAGMVHVDTDYREGCRIVVELPFSAST C1DMA9 2.7.13.3 Nif-specific regulatory protein Azotobacter vinelandii DJ 0.05897919099999999
A hexahistidine tag was appended directly to the C-terminus of the wild-type sequence
1 Escherichia coli BL21(DE3) LEVO MNATIPQRSAKQNPVELYDLQLQALASIARTLSREQQIDELLEQVLAVLHNDLGLLHGLVTISDPEHGALQIGAIHTDSE AVAQACEGVRYRSGEGVIGNVLKHGNSVVLGRISADPRFLDRLALYDLEMPFIAVPIKNPEGNTIGVLAAQPDCRADEHM PARTRLLEIVANLLAQTVRLVVNIEDGREAADERDELRREVRGKYGFENMVVGHTPTMRRVFDQIRRVAKWNSTVLVLGE SGTGKELIASAIHYNSPRAHRPFVRLNCAALPETLLESELFGHEKGAFTGAVKQRKGRFEQADGGTLFLDEIGEISPMFQ AKLLRVLQEGEFERVGGNQTVRVNVRIVAATNRDLESEVEKGKFREDLYYRLNVMAIRIPPLRERTADIPELAEFLLGKI GRQQGRPLTVTDSAIRLLMSHRWPGNVRELENCLERSAIMSEDGTITRDVVSLTGVDNESPPLAAPLPEVNLADETLDDR ERVIAALEQAGWVQAKAARLLGMTPRQIAYRIQTLNIHMRKIHHHHHH C1DMB0 FLAVIN-ADENINE DINUCLEOTIDE 0.0007855499999999999 2 FAD ADENOSINE-5'-DIPHOSPHATE 0.000427201 3 ADP singleParticle particle 1.2 7.5
20 mM HEPES pH 7.5, 300 mM NaCl, 2.5 mM MgCl2, 1 mM ADP, 1 mM TCEP
 Quantifoil R2/2 COPPER 300 CARBON HOLEY GLOW DISCHARGE
glow discharged for 60 seconds at 8 mA using an ACE 200 (Leica Microsystems)
 ETHANE 100 277 FEI VITROBOT MARK IV
The particles had a tendency to aggregate, were prone to orientational bias and because they were long and thin, they were difficult to distinguish from the background.
 TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 0.7000000000000001 2.2 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 80.0 80.0 GATAN K3 (6k x 4k) 5760 4092 1 14218 2.27 50.0
mode: counting; super resolution, x2 binning, magnified pixel size 0.83 Angstrom
 1 2186245
Used template-based picking with 2D-classes from blob picker
 cryoSPARC 4.5.3 PHASE FLIPPING AND AMPLITUDE CORRECTION AlphaFold3 model 1 C1 FOURIER SPACE 6.45 FSC 0.143 CUT-OFF cryoSPARC 4.5.3 209009 MAXIMUM LIKELIHOOD cryoSPARC 4.5.3 MAXIMUM LIKELIHOOD cryoSPARC 4.5.3 4 52252.0 cryoSPARC 4.5.3 emd_53294.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 168 168 168 0 0 0 168 168 168 249.2952 249.2952 249.2952 90.0 90.0 90.0 X Y Z -0.24982455 0.6893031 -0.0005880738 0.024454223 1.4839 1.4839 1.4839 0.06 AUTHOR Sharpened map at 6.45 A resolution used for model building and refinement AlphaFold in silico model OTHER
Real space refinement in COOT and PHENIX
cross-correlation coefficient REAL 456.0 emd_53294_msk_1.map emd_53294_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 168 168 168 0 0 0 168 168 168 249.2952 249.2952 249.2952 90.0 90.0 90.0 X Y Z -0.15591699 0.5113024 -0.0005880739 0.020855358 1.4839 1.4839 1.4839 AUTHOR Unsharpened map emd_53294_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 168 168 168 0 0 0 168 168 168 249.2952 249.2952 249.2952 90.0 90.0 90.0 X Y Z -0.16246586 0.5114601 0.0001492248 0.021513479 1.4839 1.4839 1.4839 AUTHOR Half map 1 emd_53294_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 168 168 168 0 0 0 168 168 168 249.2952 249.2952 249.2952 90.0 90.0 90.0 X Y Z -0.16164471 0.5173466 0.00012937679 0.021548472 1.4839 1.4839 1.4839 AUTHOR Half map 2