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- PDB-5l4g: The human 26S proteasome at 3.9 A -

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Basic information

Entry
Database: PDB / ID: 5l4g
TitleThe human 26S proteasome at 3.9 A
Components
  • (26S protease regulatory subunit ...) x 6
  • (Proteasome subunit alpha type- ...) x 7
  • (Proteasome subunit beta type- ...) x 7
KeywordsHYDROLASE / proteostasis / AAA-ATPase
Function / homology
Function and homology information


thyrotropin-releasing hormone receptor binding / nuclear proteasome complex / host-mediated perturbation of viral transcription / positive regulation of inclusion body assembly / proteasome accessory complex / purine ribonucleoside triphosphate binding / cytosolic proteasome complex / positive regulation of proteasomal protein catabolic process / proteasome-activating activity / proteasome regulatory particle, base subcomplex ...thyrotropin-releasing hormone receptor binding / nuclear proteasome complex / host-mediated perturbation of viral transcription / positive regulation of inclusion body assembly / proteasome accessory complex / purine ribonucleoside triphosphate binding / cytosolic proteasome complex / positive regulation of proteasomal protein catabolic process / proteasome-activating activity / proteasome regulatory particle, base subcomplex / negative regulation of programmed cell death / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / proteasome core complex / Somitogenesis / transcription factor binding / myofibril / general transcription initiation factor binding / blastocyst development / positive regulation of RNA polymerase II transcription preinitiation complex assembly / NF-kappaB binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome assembly / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / immune system process / inclusion body / ERAD pathway / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / NIK-->noncanonical NF-kB signaling / SCF-beta-TrCP mediated degradation of Emi1 / proteasome complex / proteolysis involved in protein catabolic process / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / TBP-class protein binding / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Dectin-1 mediated noncanonical NF-kB signaling / sarcomere / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Degradation of AXIN / Hh mutants are degraded by ERAD / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / G2/M Checkpoints / Defective CFTR causes cystic fibrosis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Negative regulation of NOTCH4 signaling / Vif-mediated degradation of APOBEC3G / Regulation of RUNX3 expression and activity / Hedgehog 'on' state / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / MAPK6/MAPK4 signaling / Degradation of beta-catenin by the destruction complex / lipopolysaccharide binding / negative regulation of inflammatory response to antigenic stimulus / ABC-family proteins mediated transport / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / P-body / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / response to virus / Regulation of RUNX2 expression and activity / nuclear matrix / cytoplasmic ribonucleoprotein granule / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / KEAP1-NFE2L2 pathway / UCH proteinases / osteoblast differentiation / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / peptidase activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs / ER-Phagosome pathway / response to oxidative stress
Similarity search - Function
: / 26S proteasome regulatory subunit 7, OB domain / : / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / Proteasome subunit alpha 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 ...: / 26S proteasome regulatory subunit 7, OB domain / : / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / Proteasome subunit alpha 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha5 / Proteasome subunit alpha6 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / Proteasome B-type subunit / Proteasome beta-type subunit profile. / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Nucleophile aminohydrolases, N-terminal / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Proteasome subunit alpha type-7 / 26S proteasome regulatory subunit 6A / Proteasome subunit beta type-1 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-4 / Proteasome subunit alpha type-5 ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Proteasome subunit alpha type-7 / 26S proteasome regulatory subunit 6A / Proteasome subunit beta type-1 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-4 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-4 / Proteasome subunit beta type-6 / Proteasome subunit beta type-5 / 26S proteasome regulatory subunit 7 / 26S proteasome regulatory subunit 6B / Proteasome subunit beta type-3 / Proteasome subunit beta type-2 / Proteasome subunit alpha type-6 / 26S proteasome regulatory subunit 4 / 26S proteasome regulatory subunit 8 / 26S proteasome regulatory subunit 10B / Proteasome subunit beta type-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsSchweitzer, A. / Aufderheide, A. / Rudack, T. / Beck, F.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2016
Title: Structure of the human 26S proteasome at a resolution of 3.9 Å.
Authors: Andreas Schweitzer / Antje Aufderheide / Till Rudack / Florian Beck / Günter Pfeifer / Jürgen M Plitzko / Eri Sakata / Klaus Schulten / Friedrich Förster / Wolfgang Baumeister /
Abstract: Protein degradation in eukaryotic cells is performed by the Ubiquitin-Proteasome System (UPS). The 26S proteasome holocomplex consists of a core particle (CP) that proteolytically degrades ...Protein degradation in eukaryotic cells is performed by the Ubiquitin-Proteasome System (UPS). The 26S proteasome holocomplex consists of a core particle (CP) that proteolytically degrades polyubiquitylated proteins, and a regulatory particle (RP) containing the AAA-ATPase module. This module controls access to the proteolytic chamber inside the CP and is surrounded by non-ATPase subunits (Rpns) that recognize substrates and deubiquitylate them before unfolding and degradation. The architecture of the 26S holocomplex is highly conserved between yeast and humans. The structure of the human 26S holocomplex described here reveals previously unidentified features of the AAA-ATPase heterohexamer. One subunit, Rpt6, has ADP bound, whereas the other five have ATP in their binding pockets. Rpt6 is structurally distinct from the other five Rpt subunits, most notably in its pore loop region. For Rpns, the map reveals two main, previously undetected, features: the C terminus of Rpn3 protrudes into the mouth of the ATPase ring; and Rpn1 and Rpn2, the largest proteasome subunits, are linked by an extended connection. The structural features of the 26S proteasome observed in this study are likely to be important for coordinating the proteasomal subunits during substrate processing.
History
DepositionMay 25, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Aug 2, 2017Group: Data collection / Derived calculations
Category: em_image_scans / em_software ...em_image_scans / em_software / pdbx_struct_conn_angle / struct_conf / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _em_software.name
Revision 1.3Dec 11, 2019Group: Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.ls_d_res_high / _refine.ls_d_res_low / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

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Assembly

Deposited unit
N: Proteasome subunit alpha type-6
O: Proteasome subunit alpha type-2
P: Proteasome subunit alpha type-4
Q: Proteasome subunit alpha type-7
R: Proteasome subunit alpha type-5
S: Proteasome subunit alpha type-1
T: Proteasome subunit alpha type-3
U: Proteasome subunit beta type-1
V: Proteasome subunit beta type-2
W: Proteasome subunit beta type-3
X: Proteasome subunit beta type-4
Y: Proteasome subunit beta type-5
Z: Proteasome subunit beta type-6
8: Proteasome subunit beta type-7
A: Proteasome subunit alpha type-6
B: Proteasome subunit alpha type-2
C: Proteasome subunit alpha type-4
D: Proteasome subunit alpha type-7
E: Proteasome subunit alpha type-5
F: Proteasome subunit alpha type-1
G: Proteasome subunit alpha type-3
1: Proteasome subunit beta type-1
2: Proteasome subunit beta type-2
3: Proteasome subunit beta type-3
4: Proteasome subunit beta type-4
5: Proteasome subunit beta type-5
6: Proteasome subunit beta type-6
7: Proteasome subunit beta type-7
H: 26S protease regulatory subunit 7
I: 26S protease regulatory subunit 4
K: 26S protease regulatory subunit 6B
L: 26S protease regulatory subunit 10B
M: 26S protease regulatory subunit 6A
J: 26S protease regulatory subunit 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,049,26545
Polymers1,046,18034
Non-polymers3,08511
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area170570 Å2
ΔGint-649 kcal/mol
Surface area300620 Å2
MethodPISA

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Components

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Proteasome subunit alpha type- ... , 7 types, 14 molecules NAOBPCQDRESFTG

#1: Protein Proteasome subunit alpha type-6 / 27 kDa prosomal protein / p27K / Macropain iota chain / Multicatalytic endopeptidase complex iota ...27 kDa prosomal protein / p27K / Macropain iota chain / Multicatalytic endopeptidase complex iota chain / Proteasome iota chain


Mass: 27432.459 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P60900, proteasome endopeptidase complex
#2: Protein Proteasome subunit alpha type-2 / Macropain subunit C3 / Multicatalytic endopeptidase complex subunit C3 / Proteasome component C3


Mass: 25927.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P25787, proteasome endopeptidase complex
#3: Protein Proteasome subunit alpha type-4 / Macropain subunit C9 / Multicatalytic endopeptidase complex subunit C9 / Proteasome component C9 / ...Macropain subunit C9 / Multicatalytic endopeptidase complex subunit C9 / Proteasome component C9 / Proteasome subunit L


Mass: 29525.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P25789, proteasome endopeptidase complex
#4: Protein Proteasome subunit alpha type-7 / Proteasome subunit RC6-1 / Proteasome subunit XAPC7


Mass: 27929.891 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: O14818, proteasome endopeptidase complex
#5: Protein Proteasome subunit alpha type-5 / Macropain zeta chain / Multicatalytic endopeptidase complex zeta chain / Proteasome zeta chain


Mass: 26435.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P28066, proteasome endopeptidase complex
#6: Protein Proteasome subunit alpha type-1 / 30 kDa prosomal protein / PROS-30 / Macropain subunit C2 / Multicatalytic endopeptidase complex ...30 kDa prosomal protein / PROS-30 / Macropain subunit C2 / Multicatalytic endopeptidase complex subunit C2 / Proteasome component C2 / Proteasome nu chain


Mass: 29595.627 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P25786, proteasome endopeptidase complex
#7: Protein Proteasome subunit alpha type-3 / Macropain subunit C8 / Multicatalytic endopeptidase complex subunit C8 / Proteasome component C8


Mass: 28469.252 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P25788, proteasome endopeptidase complex

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Proteasome subunit beta type- ... , 7 types, 14 molecules U1V2W3X4Y5Z687

#8: Protein Proteasome subunit beta type-1 / Macropain subunit C5 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / ...Macropain subunit C5 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / Proteasome gamma chain


Mass: 26522.396 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P20618, proteasome endopeptidase complex
#9: Protein Proteasome subunit beta type-2 / Macropain subunit C7-I / Multicatalytic endopeptidase complex subunit C7-I / Proteasome component C7-I


Mass: 22864.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMB2 / Production host: Homo sapiens (human)
References: UniProt: P49721, proteasome endopeptidase complex
#10: Protein Proteasome subunit beta type-3 / Proteasome chain 13 / Proteasome component C10-II / Proteasome theta chain


Mass: 22972.896 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P49720, proteasome endopeptidase complex
#11: Protein Proteasome subunit beta type-4 / 26 kDa prosomal protein / PROS-26 / Macropain beta chain / Multicatalytic endopeptidase complex ...26 kDa prosomal protein / PROS-26 / Macropain beta chain / Multicatalytic endopeptidase complex beta chain / Proteasome beta chain / Proteasome chain 3 / HsN3


Mass: 29231.178 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P28070, proteasome endopeptidase complex
#12: Protein Proteasome subunit beta type-5 / Macropain epsilon chain / Multicatalytic endopeptidase complex epsilon chain / Proteasome chain 6 / ...Macropain epsilon chain / Multicatalytic endopeptidase complex epsilon chain / Proteasome chain 6 / Proteasome epsilon chain / Proteasome subunit MB1 / Proteasome subunit X


Mass: 28510.248 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P28074, proteasome endopeptidase complex
#13: Protein Proteasome subunit beta type-6 / Macropain delta chain / Multicatalytic endopeptidase complex delta chain / Proteasome delta chain / ...Macropain delta chain / Multicatalytic endopeptidase complex delta chain / Proteasome delta chain / Proteasome subunit Y


Mass: 25377.652 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P28072, proteasome endopeptidase complex
#14: Protein Proteasome subunit beta type-7 / Macropain chain Z / Multicatalytic endopeptidase complex chain Z / Proteasome subunit Z


Mass: 30000.418 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q99436, proteasome endopeptidase complex

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26S protease regulatory subunit ... , 6 types, 6 molecules HIKLMJ

#15: Protein 26S protease regulatory subunit 7 / 26S proteasome AAA-ATPase subunit RPT1 / Proteasome 26S subunit ATPase 2 / Protein MSS1


Mass: 48700.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P35998
#16: Protein 26S protease regulatory subunit 4 / P26s4 / 26S proteasome AAA-ATPase subunit RPT2 / Proteasome 26S subunit ATPase 1


Mass: 49260.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62191
#17: Protein 26S protease regulatory subunit 6B / 26S proteasome AAA-ATPase subunit RPT3 / MB67-interacting protein / MIP224 / Proteasome 26S subunit ...26S proteasome AAA-ATPase subunit RPT3 / MB67-interacting protein / MIP224 / Proteasome 26S subunit ATPase 4 / Tat-binding protein 7 / TBP-7


Mass: 47426.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P43686
#18: Protein 26S protease regulatory subunit 10B / 26S proteasome AAA-ATPase subunit RPT4 / Proteasome 26S subunit ATPase 6 / Proteasome subunit p42


Mass: 44241.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62333
#19: Protein 26S protease regulatory subunit 6A / 26S proteasome AAA-ATPase subunit RPT5 / Proteasome 26S subunit ATPase 3 / Proteasome subunit P50 / ...26S proteasome AAA-ATPase subunit RPT5 / Proteasome 26S subunit ATPase 3 / Proteasome subunit P50 / Tat-binding protein 1 / TBP-1


Mass: 49266.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P17980
#20: Protein 26S protease regulatory subunit 8 / 26S proteasome AAA-ATPase subunit RPT6 / Proteasome 26S subunit ATPase 5 / Proteasome subunit p45 / ...26S proteasome AAA-ATPase subunit RPT6 / Proteasome 26S subunit ATPase 5 / Proteasome subunit p45 / Thyroid hormone receptor-interacting protein 1 / TRIP1 / p45/SUG


Mass: 45694.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62195

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Non-polymers , 3 types, 11 molecules

#21: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#22: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#23: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: human 26S proteasome / Type: COMPLEX / Entity ID: #1-#20 / Source: NATURAL
Molecular weightValue: 2.5 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse.
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingAverage exposure time: 1.5 sec. / Electron dose: 45 e/Å2 / Film or detector model: OTHER / Num. of grids imaged: 19 / Num. of real images: 40211

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Processing

SoftwareName: PHENIX / Version: (1.10.1_2155: ???) / Classification: refinement
EM software
IDNameVersionCategory
1TOM Toolboxparticle selection
4CTFFIND4CTF correction
7MDFFmodel fitting
12RELION1.43D reconstruction
13PHENIXmodel refinement
Image processingDetails: Falcon III
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 688742
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 461402 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
RefinementResolution: 3.9→3.9 Å / SU ML: 0.43 / σ(F): 1.36 / Phase error: 20.73 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2053 105155 2.5 %
Rwork0.2033 --
obs0.2033 4203206 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00768568
ELECTRON MICROSCOPYf_angle_d0.86792569
ELECTRON MICROSCOPYf_dihedral_angle_d15.61441790
ELECTRON MICROSCOPYf_chiral_restr0.04710403
ELECTRON MICROSCOPYf_plane_restr0.00611976
Refinement TLS params.

Method: refined / Refine-ID: ELECTRON MICROSCOPY

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.20450.5350.18922.30770.63733.1374-0.1961-0.64160.2190.4896-0.11080.3156-0.2573-0.26890.15230.37530.08580.07260.4738-0.04930.4306201.5406280.2895290.9689
22.5644-0.0731-1.16924.59191.00353.1042-0.2845-0.29260.52550.39250.11630.3047-0.36020.11120.14510.44930.1343-0.08380.2845-0.01340.509203.8203298.912266.9078
32.99890.352-0.73913.0051-0.68312.481-0.16960.10920.7193-0.13170.18890.4739-0.6295-0.28410.03780.48720.1109-0.12230.44710.05140.5345202.1466293.8148235.5695
44.7313-0.2267-0.07073.1286-0.17224.5496-0.06640.88960.5594-0.86120.136-0.03990.0661-0.2545-0.03340.4261-0.02620.01810.4640.09160.4755199.9678265.0411219.9153
53.17180.2656-0.3592.37241.10142.5571-0.18810.4137-0.3122-0.2506-0.10180.17860.1384-0.27970.30610.3867-0.0505-0.01450.43130.07060.4073199.5631236.9594235.0158
63.428-0.48380.30144.9839-1.0011.8456-0.3051-0.015-0.6324-0.16990.090.34050.4046-0.19980.24110.3662-0.0830.15840.4287-0.04150.4216199.2248229.1361265.5938
72.7855-0.07320.84093.4767-1.27843.9568-0.1772-0.3704-0.46570.66510.31750.5280.3596-0.4317-0.09380.49690.02770.21530.39680.0460.4743200.3577247.6836290.6389
84.5833-1.14810.41223.37490.52772.8696-0.6774-0.3608-0.83590.35130.3069-0.28650.91560.2579-0.05790.3225-0.3098-0.08690.2299-0.05180.3686240.2612224.089252.9601
94.9197-1.4684-2.28872.8332-1.38814.46960.04480.5815-0.2185-0.4269-0.0880.1671-0.1344-0.11710.1090.3768-0.0497-0.17810.29520.00420.3163241.121272.9841221.7282
104.34710.499-1.36755.97411.10642.2609-0.03740.12620.4516-0.2972-0.0925-0.0828-0.46850.07330.10110.48330.0636-0.12790.18080.12770.3691242.6118296.9367244.1567
115.17110.06381.46753.2888-1.00931.0671-0.1127-0.48-0.23120.3147-0.12420.0490.2390.22580.21570.4811-0.05090.16580.33430.01440.2377242.1811236.2752284.0675
124.8668-1.00590.331.8687-0.52124.2224-0.09220.1002-0.2427-0.07260.13080.0780.1071-0.1207-0.11850.1735-0.1784-0.07870.295-0.09770.382239.8196240.0624225.814
135.14561.11440.5362.2403-1.33453.1327-0.0863-0.35030.06010.3380.06570.0334-0.19730.02830.08290.41090.01380.18710.3122-0.1320.2754241.7602267.311294.3989
141.58570.2593-0.3281.37641.59643.19830.01210.18650.37690.17540.2402-0.0708-0.6199-0.069-0.15990.45430.0728-0.02730.3075-0.01190.4757243.0232296.0313272.0273
153.9587-0.5047-0.30313.7318-1.50712.033-0.6633-0.08750.7590.06290.51820.1914-0.6812-0.04770.00210.6434-0.45810.02470.3711-0.03080.5514277.0058297.2208252.361
165.5267-0.81072.11093.17720.88283.1451-0.05150.54350.2456-0.3132-0.0802-0.22680.2070.0520.08220.344-0.00660.21320.34220.02110.3022275.5012248.1928221.4816
174.49290.26081.84535.9246-0.15442.7412-0.04670.0689-0.3710.0563-0.1550.05920.27460.03780.26830.41520.13940.07560.2879-0.09220.3698274.4823224.3733244.1437
184.15460.0441-0.89122.88060.49592.2699-0.1669-0.78910.26890.2823-0.0408-0.1024-0.28130.15040.22820.5709-0.1768-0.09920.3428-0.10650.4055275.7463285.1688283.5982
194.8914-1.33410.4441.20760.71565.0539-0.03640.32750.4096-0.26320.0458-0.2175-0.17440.3264-0.08510.436-0.28560.10140.30750.10970.4644276.8336281.1676225.3296
203.84190.70910.08312.17421.55054.2042-0.1447-0.4121-0.07720.30120.0694-0.18170.06790.03970.05050.42790.03-0.22720.42530.09210.2997276.3172254.1606294.1522
211.34840.29770.41510.5844-0.93973.48390.04710.0895-0.33670.03630.0991-0.00090.42630.0635-0.14430.41640.2181-0.01850.3790.01220.5354274.6765225.3894271.983
223.250.4362-0.47022.1759-0.27463.3956-0.2282-0.4755-0.14420.64130.0172-0.57460.27720.48220.2110.61320.1484-0.21610.82970.03610.5872316.4957241.1359290.0806
233.36260.25550.59623.4378-0.38733.0434-0.1998-0.6107-0.53950.3939-0.0231-0.70840.42570.4310.20580.51830.1781-0.08190.71070.08620.5882313.6415222.3616266.1926
242.84270.56960.77932.69290.53882.8321-0.2010.0595-0.5916-0.15120.2667-0.68780.67780.5199-0.03050.61820.18350.10820.7074-0.04480.656314.7661227.376234.7848
253.9309-0.7469-0.60733.45170.40824.8012-0.13271.0323-0.3428-1.04910.2036-0.28110.08150.8328-0.05860.6958-0.15460.14450.8103-0.08380.66316.6206256.1289218.9618
264.097-0.7019-0.45622.797-0.40711.9342-0.14310.38930.4639-0.3688-0.0036-0.3983-0.35340.41710.12460.6908-0.24160.08880.7381-0.05790.5983317.3811284.2085233.8901
272.9309-0.4206-0.07433.7515-0.09842.019-0.1891-0.00020.8210.08350.0384-0.7289-0.51640.49880.1670.6634-0.3024-0.06470.7605-0.05020.7929318.2872292.2234264.239
282.4301-0.303-0.72282.50420.48322.7672-0.1166-0.45060.51770.60750.1522-0.6764-0.20410.6599-0.07490.6355-0.0809-0.25190.8709-0.07770.7323317.758273.7697289.3856
292.1970.0011-1.66032.22510.52286.0870.00160.1882-0.2536-0.09180.14390.63940.14-0.5538-0.16780.3155-0.0371-0.12550.67950.02610.7648163.1994247.7786249.4208
302.25730.4095-0.78665.1708-1.49744.26110.16610.42430.4277-0.276-0.39170.1723-0.2294-0.17290.15320.39730.1227-0.04210.77290.020.7576165.3044275.5338231.8285
311.47450.1272-0.23564.29461.81253.4080.02090.1430.1086-0.04510.0482-0.378-0.3802-0.0997-0.01180.61280.1285-0.03060.80430.23820.7693162.2371304.0736246.4576
322.82850.15271.76164.17820.07783.525-0.16030.11950.43460.41690.1706-0.0154-0.55360.3201-0.0490.8390.07840.14520.60230.05730.6255158.8472304.0257280.1538
331.1590.251-0.03273.68941.9153.1255-0.265-0.5966-0.03881.22790.3021-0.51380.2228-0.04880.07870.91570.213-0.22640.8536-0.02440.7506163.362277.2622297.2853
342.4509-2.5369-1.08844.83230.65022.7797-0.5108-0.2831-0.35630.65450.47630.15180.0829-0.31390.02740.6028-0.0494-0.06980.66830.13640.7458163.18248.3556282.3016
353.6287-1.0023-0.99540.90630.31285.47820.1640.5683-0.5543-0.74780.15430.70350.8093-0.3192-0.48431.6067-0.17240.28470.8927-0.10241.4913124.783258.5415259.3213
361.9726-1.1453-1.87571.02080.32412.56080.01130.7245-0.269-1.3314-0.1680.35550.6658-0.57980.06792.2435-0.31150.291.3464-0.14561.4124123.5468260.7508240.5954
370.6752-0.15770.76060.962-0.58552.9202-0.33290.51230.4008-0.22540.20320.23080.01-1.23630.12721.13750.0782-0.28231.1941-0.03011.1753111.8346298.6507250.3812
384.270.21770.5792.1111-0.55220.3954-0.6518-0.02640.3268-0.37860.50010.5768-0.8605-1.35930.08181.13920.4139-0.29541.40940.10620.993110.0627307.0162263.7915
390.88440.77-0.42161.8755-1.27943.7480.031-1.5284-0.43911.0665-0.11290.86380.9858-0.45550.19521.81270.14750.59361.81560.29961.3797115.3219276.6902303.9052
402.0450.95990.0680.947-1.13932.87370.1555-1.0307-0.47251.8885-0.54330.55280.5424-1.48190.2652.2441-0.22480.87342.08930.1991.3807115.1526268.0774307.6142
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1ELECTRON MICROSCOPY1chain A
2ELECTRON MICROSCOPY2chain B
3ELECTRON MICROSCOPY3chain C
4ELECTRON MICROSCOPY4chain D
5ELECTRON MICROSCOPY5chain E
6ELECTRON MICROSCOPY6chain F
7ELECTRON MICROSCOPY7chain G
8ELECTRON MICROSCOPY8chain 1
9ELECTRON MICROSCOPY9chain 2
10ELECTRON MICROSCOPY10chain 3
11ELECTRON MICROSCOPY11chain 4
12ELECTRON MICROSCOPY12chain 5
13ELECTRON MICROSCOPY13chain 6
14ELECTRON MICROSCOPY14chain 7
15ELECTRON MICROSCOPY15chain U
16ELECTRON MICROSCOPY16chain V
17ELECTRON MICROSCOPY17chain W
18ELECTRON MICROSCOPY18chain X
19ELECTRON MICROSCOPY19chain Y
20ELECTRON MICROSCOPY20chain Z
21ELECTRON MICROSCOPY21chain 8
22ELECTRON MICROSCOPY22chain N
23ELECTRON MICROSCOPY23chain O
24ELECTRON MICROSCOPY24chain P
25ELECTRON MICROSCOPY25chain Q
26ELECTRON MICROSCOPY26chain R
27ELECTRON MICROSCOPY27chain S
28ELECTRON MICROSCOPY28chain T
29ELECTRON MICROSCOPY29(chain H and resseq 161:433 ) or chain u
30ELECTRON MICROSCOPY30(chain I and resseq 170:434 ) or chain v
31ELECTRON MICROSCOPY31(chain J and resseq 133:397 ) or chain w
32ELECTRON MICROSCOPY32(chain K and resseq 152:411 ) or chain x
33ELECTRON MICROSCOPY33(chain L and resseq 117:379 ) or chain y
34ELECTRON MICROSCOPY34(chain M and resseq 170:431 ) or chain z
35ELECTRON MICROSCOPY35(chain H and resseq 1:160 )
36ELECTRON MICROSCOPY36(chain I and resseq 1:169 )
37ELECTRON MICROSCOPY37(chain J and resseq 1:132 )
38ELECTRON MICROSCOPY38(chain K and resseq 1:151 )
39ELECTRON MICROSCOPY39(chain L and resseq 1:116 )
40ELECTRON MICROSCOPY40(chain M and resseq 1:169 )

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