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- EMDB-31925: The motor-nucleosome module of human chromatin remodeling PBAF-nu... -

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Entry
Database: EMDB / ID: EMD-31925
TitleThe motor-nucleosome module of human chromatin remodeling PBAF-nucleosome complex
Map dataThe motor-nucleosome module of human chromatin remodeling PBAF-nucleosome complex
Sample
  • Complex: The motor-nucleosome module of human chromatin remodeling PBAF-nucleosome complex
    • Protein or peptide: Isoform 2 of Transcription activator BRG1
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B 1.1
    • Protein or peptide: Histone H3
    • DNA: DNA (207-MER)
    • DNA: DNA (207-MER)
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Keywordscomplex / DNA BINDING PROTEIN
Function / homology
Function and homology information


positive regulation of glucose mediated signaling pathway / bBAF complex / nBAF complex / npBAF complex / perichromatin fibrils / negative regulation of androgen receptor signaling pathway / GBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / neural retina development / Formation of the embryonic stem cell BAF (esBAF) complex ...positive regulation of glucose mediated signaling pathway / bBAF complex / nBAF complex / npBAF complex / perichromatin fibrils / negative regulation of androgen receptor signaling pathway / GBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / neural retina development / Formation of the embryonic stem cell BAF (esBAF) complex / EGR2 and SOX10-mediated initiation of Schwann cell myelination / Formation of the canonical BAF (cBAF) complex / RSC-type complex / Formation of the polybromo-BAF (pBAF) complex / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / Formation of the non-canonical BAF (ncBAF) complex / regulation of G0 to G1 transition / RNA polymerase I preinitiation complex assembly / Tat protein binding / host-mediated activation of viral transcription / SWI/SNF complex / ATP-dependent chromatin remodeler activity / positive regulation of T cell differentiation / regulation of mitotic metaphase/anaphase transition / nuclear androgen receptor binding / regulation of nucleotide-excision repair / positive regulation of stem cell population maintenance / lncRNA binding / positive regulation of double-strand break repair / Regulation of MITF-M-dependent genes involved in pigmentation / negative regulation of cell differentiation / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Differentiation of naive CD4+ T cells to T helper 2 cells (Th2 cells) / positive regulation of myoblast differentiation / ATP-dependent activity, acting on DNA / positive regulation of Wnt signaling pathway / positive regulation of signal transduction by p53 class mediator / regulation of G1/S transition of mitotic cell cycle / Chromatin modifying enzymes / DNA polymerase binding / helicase activity / Interleukin-7 signaling / transcription initiation-coupled chromatin remodeling / transcription coregulator binding / positive regulation of cell differentiation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / euchromatin / negative regulation of cell growth / positive regulation of miRNA transcription / Negative Regulation of CDH1 Gene Transcription / fibrillar center / Formation of the beta-catenin:TCF transactivating complex / kinetochore / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / nucleosomal DNA binding / nuclear matrix / RMTs methylate histone arginines / innate immune response in mucosa / p53 binding / transcription corepressor activity / structural constituent of chromatin / nervous system development / nucleosome / nucleosome assembly / positive regulation of cold-induced thermogenesis / chromatin organization / antimicrobial humoral immune response mediated by antimicrobial peptide / heterochromatin formation / histone binding / antibacterial humoral response / transcription coactivator activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / protein heterodimerization activity / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / nucleolus / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / : / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / protein-containing complex / DNA binding / nucleoplasm / extracellular region / ATP binding / membrane / identical protein binding / nucleus
Similarity search - Function
SWI/SNF complex subunit BRG1 / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / QLQ / Glutamine-Leucine-Glutamine, QLQ / QLQ domain profile. / QLQ / Snf2-ATP coupling, chromatin remodelling complex ...SWI/SNF complex subunit BRG1 / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / QLQ / Glutamine-Leucine-Glutamine, QLQ / QLQ domain profile. / QLQ / Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / domain in helicases and associated with SANT domains / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Helicase conserved C-terminal domain / Histone H3 signature 1. / Histone H3 signature 2. / Bromodomain, conserved site / Bromodomain signature. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Histone-fold / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Histone H3 / Histone H2B 1.1 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4 / Histone H4 / Histone H2A
Similarity search - Component
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsChen ZC / Chen KJ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nature / Year: 2022
Title: Structure of human chromatin-remodelling PBAF complex bound to a nucleosome.
Authors: Junjie Yuan / Kangjing Chen / Wenbo Zhang / Zhucheng Chen /
Abstract: DNA wraps around the histone octamer to form nucleosomes, the repeating unit of chromatin, which create barriers for accessing genetic information. Snf2-like chromatin remodellers couple the energy ...DNA wraps around the histone octamer to form nucleosomes, the repeating unit of chromatin, which create barriers for accessing genetic information. Snf2-like chromatin remodellers couple the energy of ATP binding and hydrolysis to reposition and recompose the nucleosome, and have vital roles in various chromatin-based transactions. Here we report the cryo-electron microscopy structure of the 12-subunit human chromatin-remodelling polybromo-associated BRG1-associated factor (PBAF) complex bound to the nucleosome. The motor subunit SMARCA4 engages the nucleosome in the active conformation, which reveals clustering of multiple disease-associated mutations at the interfaces that are essential for chromatin-remodelling activity. SMARCA4 recognizes the H2A-H2B acidic pocket of the nucleosome through three arginine anchors of the Snf2 ATP coupling (SnAc) domain. PBAF shows notable functional modularity, and most of the auxiliary subunits are interwoven into three lobe-like submodules for nucleosome recognition. The PBAF-specific auxiliary subunit ARID2 acts as the structural core for assembly of the DNA-binding lobe, whereas PBRM1, PHF10 and BRD7 are collectively incorporated into the lobe for histone tail binding. Together, our findings provide mechanistic insights into nucleosome recognition by PBAF and a structural basis for understanding SMARCA4-related human diseases.
History
DepositionSep 7, 2021-
Header (metadata) releaseMay 18, 2022-
Map releaseMay 18, 2022-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31925.png

Downloads & links

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Map

FileDownload / File: emd_31925.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe motor-nucleosome module of human chromatin remodeling PBAF-nucleosome complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 360 pix.
= 389.7 Å		1.08 Å/pix.
x 360 pix.
= 389.7 Å		1.08 Å/pix.
x 360 pix.
= 389.7 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.029721776 - 0.102493845
Average (Standard dev.)0.00008678122 (±0.0015360364)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 389.69998 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : The motor-nucleosome module of human chromatin remodeling PBAF-nu...

EntireName: The motor-nucleosome module of human chromatin remodeling PBAF-nucleosome complex
Components
  • Complex: The motor-nucleosome module of human chromatin remodeling PBAF-nucleosome complex
    • Protein or peptide: Isoform 2 of Transcription activator BRG1
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B 1.1
    • Protein or peptide: Histone H3
    • DNA: DNA (207-MER)
    • DNA: DNA (207-MER)
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: The motor-nucleosome module of human chromatin remodeling PBAF-nu...

SupramoleculeName: The motor-nucleosome module of human chromatin remodeling PBAF-nucleosome complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Isoform 2 of Transcription activator BRG1

MacromoleculeName: Isoform 2 of Transcription activator BRG1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 169.597938 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MQALGQQNRG PTPFNQNQLH QLRAQIMAYK MLARGQPLPD HLQMAVQGKR PMPGMQQQMP TLPPPSVSAT GPGPGPGPGP GPGPGPAPP NYSRPHGMGG PNMPPPGPSG VPPGMPGQPP GGPPKPWPEG PMANAAAPTS TPQKLIPPQP TGRPSPAPPA V PPAASPVM ...String:
MQALGQQNRG PTPFNQNQLH QLRAQIMAYK MLARGQPLPD HLQMAVQGKR PMPGMQQQMP TLPPPSVSAT GPGPGPGPGP GPGPGPAPP NYSRPHGMGG PNMPPPGPSG VPPGMPGQPP GGPPKPWPEG PMANAAAPTS TPQKLIPPQP TGRPSPAPPA V PPAASPVM PPQTQSPGQP AQPAPMVPLH QKQSRITPIQ KPRGLDPVEI LQEREYRLQA RIAHRIQELE NLPGSLAGDL RT KATIELK ALRLLNFQRQ LRQEVVVCMR RDTALETALN AKAYKRSKRQ SLREARITEK LEKQQKIEQE RKRRQKHQEY LNS ILQHAK DFKEYHRSVT GKIQKLTKAV ATYHANTERE QKKENERIEK ERMRRLMAED EEGYRKLIDQ KKDKRLAYLL QQTD EYVAN LTELVRQHKA AQVAKEKKKK KKKKKAENAE GQTPAIGPDG EPLDETSQMS DLPVKVIHVE SGKILTGTDA PKAGQ LEAW LEMNPGYEVA PRSDSEESGS EEEEEEEEEE QPQAAQPPTL PVEEKKKIPD PDSDDVSEVD ARHIIENAKQ DVDDEY GVS QALARGLQSY YAVAHAVTER VDKQSALMVN GVLKQYQIKG LEWLVSLYNN NLNGILADEM GLGKTIQTIA LITYLME HK RINGPFLIIV PLSTLSNWAY EFDKWAPSVV KVSYKGSPAA RRAFVPQLRS GKFNVLLTTY EYIIKDKHIL AKIRWKYM I VDEGHRMKNH HCKLTQVLNT HYVAPRRLLL TGTPLQNKLP ELWALLNFLL PTIFKSCSTF EQWFNAPFAM TGEKVDLNE EETILIIRRL HKVLRPFLLR RLKKEVEAQL PEKVEYVIKC DMSALQRVLY RHMQAKGVLL TDGSEKDKKG KGGTKTLMNT IMQLRKICN HPYMFQHIEE SFSEHLGFTG GIVQGLDLYR ASGKFELLDR ILPKLRATNH KVLLFCQMTS LMTIMEDYFA Y RGFKYLRL DGTTKAEDRG MLLKTFNEPG SEYFIFLLST RAGGLGLNLQ SADTVIIFDS DWNPHQDLQA QDRAHRIGQQ NE VRVLRLC TVNSVEEKIL AAAKYKLNVD QKVIQAGMFD QKSSSHERRA FLQAILEHEE QDEEEDEVPD DETVNQMIAR HEE EFDLFM RMDLDRRREE ARNPKRKPRL MEEDELPSWI IKDDAEVERL TCEEEEEKMF GRGSRHRKEV DYSDSLTEKQ WLKA IEEGT LEEIEEEVRQ KKSSRKRKRD SDAGSSTPTT STRSRDKDDE SKKQKKRGRP PAEKLSPNPP NLTKKMKKIV DAVIK YKDS SSGRQLSEVF IQLPSRKELP EYYELIRKPV DFKKIKERIR NHKYRSLNDL EKDVMLLCQN AQTFNLEGSL IYEDSI VLQ SVFTSVRQKI EKEDDSEGEE SEEEEEGEEE GSESESRSVK VKIKLGRKEK AQDRLKGGRR RPSRGSRAKP VVSDDDS EE EQEEDRSGSG SEEDASGGSW SHPQFEKWSH PQFEKWSHPQ FEK

UniProtKB: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 14.109436 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKQGGK TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVR NDEELNKLLG RVTIAQGGVL PNIQSVLLPK KTESSKSAKS K

UniProtKB: Histone H2A

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Macromolecule #4: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.965265 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KTQKKDGKKR RKSRKESYAI YVYKVLKQVH PDTGISSKAM SIMNSFVNDV FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSAK

UniProtKB: Histone H2B 1.1

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Macromolecule #5: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.435126 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVALFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3

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Macromolecule #6: DNA (207-MER)

MacromoleculeName: DNA (207-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 63.679574 KDa
SequenceString: (DG)(DG)(DA)(DC)(DC)(DC)(DT)(DA)(DT)(DA) (DC)(DG)(DC)(DG)(DG)(DC)(DC)(DG)(DC)(DC) (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT) (DC)(DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG) (DA) (DG)(DG)(DC)(DC)(DG)(DC) ...String:
(DG)(DG)(DA)(DC)(DC)(DC)(DT)(DA)(DT)(DA) (DC)(DG)(DC)(DG)(DG)(DC)(DC)(DG)(DC)(DC) (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT) (DC)(DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG) (DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC) (DA)(DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT) (DA)(DG) (DA)(DC)(DA)(DG)(DC)(DT)(DC) (DT)(DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT) (DT)(DA)(DA) (DA)(DC)(DG)(DC)(DA)(DC) (DG)(DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG) (DT)(DC)(DC)(DC) (DC)(DC)(DG)(DC)(DG) (DT)(DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC) (DC)(DA)(DA)(DG)(DG) (DG)(DG)(DA)(DT) (DT)(DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG) (DT)(DC)(DT)(DC)(DC)(DA) (DG)(DG)(DC) (DA)(DC)(DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT) (DC)(DC)(DT)(DG)(DA)(DA)(DG)(DC)(DT)(DT) (DG)(DT)(DC)(DG)(DA)(DG)(DA)(DA) (DG) (DT)(DA)(DC)(DT)(DA)(DG)(DA)(DG)(DG)(DA) (DT)(DC)(DA)(DT)(DA)(DA)(DT)(DC)(DA) (DG)(DC)(DC)(DA)(DT)(DA)(DC)

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Macromolecule #7: DNA (207-MER)

MacromoleculeName: DNA (207-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 64.145816 KDa
SequenceString: (DG)(DT)(DA)(DT)(DG)(DG)(DC)(DT)(DG)(DA) (DT)(DT)(DA)(DT)(DG)(DA)(DT)(DC)(DC)(DT) (DC)(DT)(DA)(DG)(DT)(DA)(DC)(DT)(DT) (DC)(DT)(DC)(DG)(DA)(DC)(DA)(DA)(DG)(DC) (DT) (DT)(DC)(DA)(DG)(DG)(DA) ...String:
(DG)(DT)(DA)(DT)(DG)(DG)(DC)(DT)(DG)(DA) (DT)(DT)(DA)(DT)(DG)(DA)(DT)(DC)(DC)(DT) (DC)(DT)(DA)(DG)(DT)(DA)(DC)(DT)(DT) (DC)(DT)(DC)(DG)(DA)(DC)(DA)(DA)(DG)(DC) (DT) (DT)(DC)(DA)(DG)(DG)(DA)(DT)(DG) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG) (DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC) (DT)(DG)(DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG) (DG)(DG)(DA) (DG)(DT)(DA)(DA)(DT)(DC) (DC)(DC)(DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG) (DT)(DT)(DA)(DA) (DA)(DA)(DC)(DG)(DC) (DG)(DG)(DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC) (DG)(DC)(DG)(DT)(DA) (DC)(DG)(DT)(DG) (DC)(DG)(DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG) (DG)(DT)(DG)(DC)(DT)(DA) (DG)(DA)(DG) (DC)(DT)(DG)(DT)(DC)(DT)(DA)(DC)(DG)(DA) (DC)(DC)(DA)(DA)(DT)(DT)(DG) (DA)(DG) (DC)(DG)(DG)(DC)(DC)(DT)(DC)(DG)(DG)(DC) (DA)(DC)(DC)(DG)(DG)(DG)(DA)(DT) (DT) (DC)(DT)(DC)(DC)(DA)(DG)(DG)(DG)(DC)(DG) (DG)(DC)(DC)(DG)(DC)(DG)(DT)(DA)(DT) (DA)(DG)(DG)(DG)(DT)(DC)(DC)

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Macromolecule #8: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Macromolecule #9: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 9 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #10: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 10 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 208905
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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