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- EMDB-3314: Rigid part of the CSN-N8-CRL4A cryo-EM structure at 6.4 A resolution -

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Entry
Database: EMDB / ID: EMD-3314
TitleRigid part of the CSN-N8-CRL4A cryo-EM structure at 6.4 A resolution
Map dataCryo-EM structure of CSN-N8-CRL4A at 6.4 A resolution
Sample
  • Sample: Recombinant human CSN-N8-CRL4A complex
  • Protein or peptide: x 12 types
KeywordsCOP9 Signalosome / Cullin-RING ligases / Cryo-EM
Function / homology
Function and homology information


Prolactin receptor signaling / regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / COP9 signalosome assembly / Regulation of BACH1 activity / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / trophectodermal cell proliferation / Dual Incision in GG-NER / Dual incision in TC-NER ...Prolactin receptor signaling / regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / COP9 signalosome assembly / Regulation of BACH1 activity / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / trophectodermal cell proliferation / Dual Incision in GG-NER / Dual incision in TC-NER / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / macrophage migration inhibitory factor binding / Regulation of RAS by GAPs / Regulation of RUNX2 expression and activity / Degradation of GLI1 by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of DVL / Orc1 removal from chromatin / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / regulation of IRE1-mediated unfolded protein response / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Hedgehog 'on' state / negative regulation of granulocyte differentiation / exosomal secretion / Degradation of beta-catenin by the destruction complex / deNEDDylase activity / GTPase inhibitor activity / eukaryotic initiation factor 4E binding / Interleukin-1 signaling / protein deneddylation / regulation of protein neddylation / anaphase-promoting complex / activation of NF-kappaB-inducing kinase activity / eukaryotic translation initiation factor 3 complex / KEAP1-NFE2L2 pathway / GLI3 is processed to GLI3R by the proteasome / Neddylation / cullin-RING-type E3 NEDD8 transferase / Antigen processing: Ubiquitination & Proteasome degradation / cullin-RING ubiquitin ligase complex / COP9 signalosome / positive regulation by virus of viral protein levels in host cell / regulation of DNA damage checkpoint / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / spindle assembly involved in female meiosis / regulation of nucleotide-excision repair / regulation of proteolysis / epigenetic programming in the zygotic pronuclei / VCB complex / Cul4-RING E3 ubiquitin ligase complex / positive regulation of protein autoubiquitination / UV-damage excision repair / protein neddylation / metal-dependent deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases) / NEDD8 ligase activity / biological process involved in interaction with symbiont / RHOBTB1 GTPase cycle / Cul5-RING ubiquitin ligase complex / negative regulation of response to oxidative stress / ubiquitin-ubiquitin ligase activity / inner cell mass cell proliferation / regulation of mitotic cell cycle phase transition / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul4B-RING E3 ubiquitin ligase complex / negative regulation of type I interferon production / ubiquitin ligase complex scaffold activity / Cul3-RING ubiquitin ligase complex / negative regulation of reproductive process / negative regulation of developmental process / skeletal muscle cell differentiation / TGF-beta receptor signaling activates SMADs / protein monoubiquitination / viral release from host cell / cullin family protein binding / somatic stem cell population maintenance / regulation of JNK cascade / hemopoiesis / ectopic germ cell programmed cell death / response to light stimulus / anatomical structure morphogenesis / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of viral genome replication / proteasomal protein catabolic process / protein K48-linked ubiquitination / ubiquitin ligase complex / JNK cascade / positive regulation of gluconeogenesis / positive regulation of TORC1 signaling / post-translational protein modification / intrinsic apoptotic signaling pathway / translation initiation factor activity / T cell activation / nucleotide-excision repair
Similarity search - Function
COP9 signalosome, subunit CSN8 / COP9 signalosome complex subunit 7, helix I / : / COP9 signalosome complex subunit 7a helix I domain / COP9 signalosome complex subunit 3-like, C-terminal helix / CSN7 helical bundle subdomain / COP9 signalosome complex subunit 3, N-terminal helical repeats / COP9 signalosome subunit 6 / : / COP9 signalosome complex subunit 1, C-terminal helix ...COP9 signalosome, subunit CSN8 / COP9 signalosome complex subunit 7, helix I / : / COP9 signalosome complex subunit 7a helix I domain / COP9 signalosome complex subunit 3-like, C-terminal helix / CSN7 helical bundle subdomain / COP9 signalosome complex subunit 3, N-terminal helical repeats / COP9 signalosome subunit 6 / : / COP9 signalosome complex subunit 1, C-terminal helix / Cop9 signalosome subunit 5 C-terminal domain / COP9 signalosome complex subunit 4, helix turn helix domain / Cop9 signalosome subunit 5 C-terminal domain / CSN4/RPN5/eIF3a helix turn helix domain / Nedd8-like ubiquitin / Eukaryotic translation initiation factor 3 subunit M eIF3m/COP9 signalosome complex subunit 7 COPS7 / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / : / : / PSMD12/CSN4, N-terminal / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 26S proteasome regulatory subunit Rpn7, N-terminal / 26S proteasome subunit RPN7 / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / PCI/PINT associated module / Cullin protein neddylation domain / : / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / : / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / : / CPSF A subunit region / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / Zinc finger RING-type profile. / Zinc finger, RING-type / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Tetratricopeptide-like helical domain superfamily / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
COP9 signalosome complex subunit 2 / E3 ubiquitin-protein ligase RBX1 / COP9 signalosome complex subunit 1 / Cullin-4A / NEDD8 / DNA damage-binding protein 1 / COP9 signalosome complex subunit 6 / COP9 signalosome complex subunit 5 / COP9 signalosome complex subunit 8 / COP9 signalosome complex subunit 4 ...COP9 signalosome complex subunit 2 / E3 ubiquitin-protein ligase RBX1 / COP9 signalosome complex subunit 1 / Cullin-4A / NEDD8 / DNA damage-binding protein 1 / COP9 signalosome complex subunit 6 / COP9 signalosome complex subunit 5 / COP9 signalosome complex subunit 8 / COP9 signalosome complex subunit 4 / COP9 signalosome complex subunit 7a / COP9 signalosome complex subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.4 Å
AuthorsCavadini S / Fischer ES / Bunker RD / Potenza A / Lingaraju GM / Goldie KN / Mohamed WI / Faty M / Petzold G / Beckwith REJ ...Cavadini S / Fischer ES / Bunker RD / Potenza A / Lingaraju GM / Goldie KN / Mohamed WI / Faty M / Petzold G / Beckwith REJ / Tichkule R / Hassiepen U / Abdulrahman W / Pantelic RS / Matsumoto S / Sugasawa K / Stahlberg H / Thoma NH
CitationJournal: Nature / Year: 2016
Title: Cullin-RING ubiquitin E3 ligase regulation by the COP9 signalosome.
Authors: Simone Cavadini / Eric S Fischer / Richard D Bunker / Alessandro Potenza / Gondichatnahalli M Lingaraju / Kenneth N Goldie / Weaam I Mohamed / Mahamadou Faty / Georg Petzold / Rohan E J ...Authors: Simone Cavadini / Eric S Fischer / Richard D Bunker / Alessandro Potenza / Gondichatnahalli M Lingaraju / Kenneth N Goldie / Weaam I Mohamed / Mahamadou Faty / Georg Petzold / Rohan E J Beckwith / Ritesh B Tichkule / Ulrich Hassiepen / Wassim Abdulrahman / Radosav S Pantelic / Syota Matsumoto / Kaoru Sugasawa / Henning Stahlberg / Nicolas H Thomä /
Abstract: The cullin-RING ubiquitin E3 ligase (CRL) family comprises over 200 members in humans. The COP9 signalosome complex (CSN) regulates CRLs by removing their ubiquitin-like activator NEDD8. The CUL4A- ...The cullin-RING ubiquitin E3 ligase (CRL) family comprises over 200 members in humans. The COP9 signalosome complex (CSN) regulates CRLs by removing their ubiquitin-like activator NEDD8. The CUL4A-RBX1-DDB1-DDB2 complex (CRL4A(DDB2)) monitors the genome for ultraviolet-light-induced DNA damage. CRL4A(DBB2) is inactive in the absence of damaged DNA and requires CSN to regulate the repair process. The structural basis of CSN binding to CRL4A(DDB2) and the principles of CSN activation are poorly understood. Here we present cryo-electron microscopy structures for CSN in complex with neddylated CRL4A ligases to 6.4 Å resolution. The CSN conformers defined by cryo-electron microscopy and a novel apo-CSN crystal structure indicate an induced-fit mechanism that drives CSN activation by neddylated CRLs. We find that CSN and a substrate cannot bind simultaneously to CRL4A, favouring a deneddylated, inactive state for substrate-free CRL4 complexes. These architectural and regulatory principles appear conserved across CRL families, allowing global regulation by CSN.
History
DepositionJan 30, 2016-
Header (metadata) releaseFeb 24, 2016-
Map releaseApr 6, 2016-
UpdateApr 13, 2016-
Current statusApr 13, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3314.png

Downloads & links

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Map

FileDownload / File: emd_3314.map.gz / Format: CCP4 / Size: 39.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of CSN-N8-CRL4A at 6.4 A resolution
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 220 pix.
= 290.4 Å		1.32 Å/pix.
x 220 pix.
= 290.4 Å		1.32 Å/pix.
x 220 pix.
= 290.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.02075368 - 0.0694446
Average (Standard dev.)-0.00006025 (±0.00419539)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-110-110-110
Dimensions220220220
Spacing220220220
CellA=B=C: 290.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z290.400290.400290.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-300-64
NX/NY/NZ6161129
MAP C/R/S123
start NC/NR/NS-110-110-110
NC/NR/NS220220220
D min/max/mean-0.0210.069-0.000

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Supplemental data

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Sample components

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Entire : Recombinant human CSN-N8-CRL4A complex

EntireName: Recombinant human CSN-N8-CRL4A complex
Components
  • Sample: Recombinant human CSN-N8-CRL4A complex
  • Protein or peptide: COP9 signalosome subunit 1
  • Protein or peptide: COP9 signalosome subunit 2
  • Protein or peptide: COP9 signalosome subunit 3
  • Protein or peptide: COP9 signalosome subunit 4
  • Protein or peptide: COP9 signalosome subunit 5
  • Protein or peptide: COP9 signalosome subunit 6
  • Protein or peptide: COP9 signalosome subunit 7A
  • Protein or peptide: COP9 signalosome subunit 8
  • Protein or peptide: CUL4A
  • Protein or peptide: DNA DAMAGE-BINDING PROTEIN 1
  • Protein or peptide: E3 UBIQUITIN-PROTEIN LIGASE RBX1
  • Protein or peptide: NEDD8

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Supramolecule #1000: Recombinant human CSN-N8-CRL4A complex

SupramoleculeName: Recombinant human CSN-N8-CRL4A complex / type: sample / ID: 1000 / Number unique components: 12
Molecular weightTheoretical: 493 KDa

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Macromolecule #1: COP9 signalosome subunit 1

MacromoleculeName: COP9 signalosome subunit 1 / type: protein_or_peptide / ID: 1 / Name.synonym: CSN1 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceUniProtKB: COP9 signalosome complex subunit 1

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Macromolecule #2: COP9 signalosome subunit 2

MacromoleculeName: COP9 signalosome subunit 2 / type: protein_or_peptide / ID: 2 / Name.synonym: CSN2 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceUniProtKB: COP9 signalosome complex subunit 2

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Macromolecule #3: COP9 signalosome subunit 3

MacromoleculeName: COP9 signalosome subunit 3 / type: protein_or_peptide / ID: 3 / Name.synonym: CSN3 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceUniProtKB: COP9 signalosome complex subunit 3

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Macromolecule #4: COP9 signalosome subunit 4

MacromoleculeName: COP9 signalosome subunit 4 / type: protein_or_peptide / ID: 4 / Name.synonym: CSN4 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.6 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceUniProtKB: COP9 signalosome complex subunit 4

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Macromolecule #5: COP9 signalosome subunit 5

MacromoleculeName: COP9 signalosome subunit 5 / type: protein_or_peptide / ID: 5 / Name.synonym: CSN5 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.4 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceUniProtKB: COP9 signalosome complex subunit 5

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Macromolecule #6: COP9 signalosome subunit 6

MacromoleculeName: COP9 signalosome subunit 6 / type: protein_or_peptide / ID: 6 / Name.synonym: CSN6 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.6 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceUniProtKB: COP9 signalosome complex subunit 6

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Macromolecule #7: COP9 signalosome subunit 7A

MacromoleculeName: COP9 signalosome subunit 7A / type: protein_or_peptide / ID: 7 / Name.synonym: CSN7A / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceUniProtKB: COP9 signalosome complex subunit 7a

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Macromolecule #8: COP9 signalosome subunit 8

MacromoleculeName: COP9 signalosome subunit 8 / type: protein_or_peptide / ID: 8 / Name.synonym: CSN8 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceUniProtKB: COP9 signalosome complex subunit 8

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Macromolecule #9: CUL4A

MacromoleculeName: CUL4A / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 79.3 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceUniProtKB: Cullin-4A

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Macromolecule #10: DNA DAMAGE-BINDING PROTEIN 1

MacromoleculeName: DNA DAMAGE-BINDING PROTEIN 1 / type: protein_or_peptide / ID: 10 / Name.synonym: DDB1 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 125.4 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceUniProtKB: DNA damage-binding protein 1

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Macromolecule #11: E3 UBIQUITIN-PROTEIN LIGASE RBX1

MacromoleculeName: E3 UBIQUITIN-PROTEIN LIGASE RBX1 / type: protein_or_peptide / ID: 11 / Name.synonym: RBX1 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.8 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceUniProtKB: E3 ubiquitin-protein ligase RBX1

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Macromolecule #12: NEDD8

MacromoleculeName: NEDD8 / type: protein_or_peptide / ID: 12 / Name.synonym: NEDD8 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.9 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: NEDD8

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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

Concentration0.1 mg/mL
BufferpH: 7.4 / Details: 50mM HEPES, 200mM NaCl, 0.25mM TCEP
GridDetails: Quantifoil holey carbon grids (R1.2/1.3, Cu 400 mesh) and Lacey carbons films
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 93 K / Instrument: LEICA EM GP / Method: Blot for 2 seconds before plunging

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: Gatan Image Filter Quantum LS / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
DateJun 1, 2015
Image recordingCategory: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 2626
Details: Every image is the average of 38 frames recorded by the direct electron detector
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.4 Å / Resolution method: OTHER / Software - Name: EMAN2, RELION / Number images used: 63269

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Atomic model buiding 1

Initial modelPDB ID:

4d10

RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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Atomic model buiding 2

Initial modelPDB ID:

4d18

RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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Atomic model buiding 3

Initial modelPDB ID:

4a0k

RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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