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Basic information

Entry
Database: PDB / ID: 5iv5
TitleCryo-electron microscopy structure of the hexagonal pre-attachment T4 baseplate-tail tube complex
Components
  • (Baseplate tail-tube protein ...) x 2
  • (Baseplate wedge protein ...) x 8
  • Baseplate hub protein gp27
  • Peptidoglycan hydrolase gp5
  • Short tail fiber protein gp12
  • Tail tube protein gp19
  • Uncharacterized 10.2 kDa protein in segC-Gp6 intergenic region
KeywordsVIRAL PROTEIN / T4 / baseplate-tail tube complex / pre-attachment / bacteriophage / bacterial virus / hexagonal / membrane-piercing / cell attachment / infection
Function / homology
Function and homology information


peptidoglycan beta-N-acetylmuramidase activity / symbiont genome ejection through host cell envelope, contractile tail mechanism / symbiont entry into host cell via disruption of host cell wall peptidoglycan / virus tail, tube / virus tail, baseplate / virus tail, fiber / viral tail assembly / symbiont entry into host cell via disruption of host cell envelope / symbiont entry into host / virus tail ...peptidoglycan beta-N-acetylmuramidase activity / symbiont genome ejection through host cell envelope, contractile tail mechanism / symbiont entry into host cell via disruption of host cell wall peptidoglycan / virus tail, tube / virus tail, baseplate / virus tail, fiber / viral tail assembly / symbiont entry into host cell via disruption of host cell envelope / symbiont entry into host / virus tail / viral release from host cell / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / entry receptor-mediated virion attachment to host cell / defense response to bacterium / symbiont entry into host cell / structural molecule activity / identical protein binding / metal ion binding
Similarity search - Function
Baseplate tail-tube protein gp48, T4-like virus / Tail-tube assembly protein / Bacteriophage T4, Gp12 / Baseplate wedge protein gp53, bacteriophage T4 / Short tail fibre protein, C-terminal / Baseplate wedge protein gp7 / Short tail fibre protein, C-terminal superfamily / : / : / : ...Baseplate tail-tube protein gp48, T4-like virus / Tail-tube assembly protein / Bacteriophage T4, Gp12 / Baseplate wedge protein gp53, bacteriophage T4 / Short tail fibre protein, C-terminal / Baseplate wedge protein gp7 / Short tail fibre protein, C-terminal superfamily / : / : / : / Phage short tail fibre protein gp12, middle domain / Base plate wedge protein 53 / Short tail fibre protein receptor-binding domain / Baseplate wedge protein gp7, domain V / Baseplate wedge protein gp7, helical domain / Baseplate wedge protein gp7, domain VI / Phage tail collar domain / Bacteriophage T4, Gp27, baseplate hub, C-terminal / Bacteriophage T4, Gp27, baseplate hub, N-terminal / Phage tail collar domain superfamily / Gp27, baseplate hub, domain 3 / Gp27, baseplate hub, domain 4 / Gp27, baseplate hub, domain 2 / Phage Tail Collar Domain / Baseplate structural protein, domain 2 / Baseplate structural protein, domain 1 / Baseplate structural protein Gp11 / Bacteriophage T4, Gp11, C-terminal finger domain / Baseplate structural protein Gp11, N-terminal domain superfamily / Baseplate structural protein Gp11 superfamily / Baseplate structural protein Gp11, C-terminal domain / GP11 baseplate wedge protein / Baseplate wedge protein gp10 / Baseplate wedge protein gp6 / : / : / : / : / : / : / Baseplate wedge protein gp6-like, helical domain / Baseplate structural protein gp6, C-terminal domain I / Baseplate structural protein gp6, C-terminal domain II / Baseplate wedge protein gp6, domain II / Baseplate structural protein gp6, C-terminal domain III / Baseplate wedge protein gp10 domain 3 / Baseplate structural protein Gp9 C-terminal domain superfamily / Bacteriophage T4, Gp8 / Bacteriophage T4, Gp8 superfamily / Bacteriophage T4, Gp8 / : / Baseplate structural protein Gp10, C-terminal domain / Baseplate structural protein Gp9/Gp10 / Baseplate structural protein Gp9/Gp10 middle domain superfamily / Gp9-like superfamily / Bacteriophage T4 gp9/10-like protein / Protein Gp5, N-terminal OB-fold domain / Gp5, C-terminal / Pre-baseplate central spike protein Gp5 / Gp5 N-terminal OB domain / Gp5 C-terminal repeat (3 copies) / PAAR motif / PAAR motif / IraD/Gp25-like / Baseplate wedge protein gp25 / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Lysozyme-like domain superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Immunoglobulin-like fold
Similarity search - Domain/homology
: / Baseplate wedge protein gp25 / Baseplate protein gp9 / Baseplate wedge protein gp10 / Baseplate wedge protein gp11 / Short tail fiber protein gp12 / Tail tube protein gp19 / Baseplate tail-tube junction protein gp48 / Baseplate tail-tube junction protein gp54 / Pre-baseplate central spike protein Gp5 ...: / Baseplate wedge protein gp25 / Baseplate protein gp9 / Baseplate wedge protein gp10 / Baseplate wedge protein gp11 / Short tail fiber protein gp12 / Tail tube protein gp19 / Baseplate tail-tube junction protein gp48 / Baseplate tail-tube junction protein gp54 / Pre-baseplate central spike protein Gp5 / Baseplate wedge protein gp53 / Baseplate central spike complex protein gp27 / Baseplate wedge protein gp6 / Baseplate wedge protein gp7 / Baseplate wedge protein gp8 / Baseplate puncturing device gp5.4
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.11 Å
AuthorsTaylor, N.M.I. / Guerrero-Ferreira, R.C. / Goldie, K.N. / Stahlberg, H. / Leiman, P.G.
CitationJournal: Nature / Year: 2016
Title: Structure of the T4 baseplate and its function in triggering sheath contraction.
Authors: Nicholas M I Taylor / Nikolai S Prokhorov / Ricardo C Guerrero-Ferreira / Mikhail M Shneider / Christopher Browning / Kenneth N Goldie / Henning Stahlberg / Petr G Leiman /
Abstract: Several systems, including contractile tail bacteriophages, the type VI secretion system and R-type pyocins, use a multiprotein tubular apparatus to attach to and penetrate host cell membranes. This ...Several systems, including contractile tail bacteriophages, the type VI secretion system and R-type pyocins, use a multiprotein tubular apparatus to attach to and penetrate host cell membranes. This macromolecular machine resembles a stretched, coiled spring (or sheath) wound around a rigid tube with a spike-shaped protein at its tip. A baseplate structure, which is arguably the most complex part of this assembly, relays the contraction signal to the sheath. Here we present the atomic structure of the approximately 6-megadalton bacteriophage T4 baseplate in its pre- and post-host attachment states and explain the events that lead to sheath contraction in atomic detail. We establish the identity and function of a minimal set of components that is conserved in all contractile injection systems and show that the triggering mechanism is universally conserved.
History
DepositionMar 19, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Jun 8, 2016Group: Database references
Revision 1.3Aug 30, 2017Group: Advisory / Data collection
Category: em_imaging_optics / em_software / pdbx_validate_polymer_linkage
Item: _em_imaging_optics.energyfilter_name / _em_software.details ..._em_imaging_optics.energyfilter_name / _em_software.details / _em_software.name / _pdbx_validate_polymer_linkage.dist / _pdbx_validate_polymer_linkage.label_alt_id_1 / _pdbx_validate_polymer_linkage.label_alt_id_2
Revision 1.4Feb 7, 2018Group: Data collection / Category: em_imaging_optics / Item: _em_imaging_optics.energyfilter_lower

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Structure visualization

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Assembly

Deposited unit
A: Baseplate wedge protein gp6
B: Baseplate wedge protein gp6
C: Baseplate wedge protein gp7
D: Baseplate wedge protein gp8
E: Baseplate wedge protein gp8
F: Baseplate wedge protein gp9
G: Baseplate wedge protein gp9
H: Baseplate wedge protein gp9
I: Baseplate wedge protein gp10
J: Baseplate wedge protein gp10
K: Baseplate wedge protein gp10
L: Baseplate wedge protein gp11
M: Baseplate wedge protein gp11
N: Baseplate wedge protein gp11
O: Short tail fiber protein gp12
P: Short tail fiber protein gp12
Q: Short tail fiber protein gp12
R: Tail tube protein gp19
S: Tail tube protein gp19
T: Baseplate wedge protein gp25
U: Baseplate tail-tube protein gp48
V: Baseplate wedge protein gp53
W: Baseplate tail-tube protein gp54
X: Baseplate wedge protein gp6
Y: Baseplate wedge protein gp6
Z: Baseplate wedge protein gp7
a: Baseplate wedge protein gp8
b: Baseplate wedge protein gp8
c: Baseplate wedge protein gp9
d: Baseplate wedge protein gp9
e: Baseplate wedge protein gp9
f: Baseplate wedge protein gp10
g: Baseplate wedge protein gp10
h: Baseplate wedge protein gp10
i: Baseplate wedge protein gp11
j: Baseplate wedge protein gp11
k: Baseplate wedge protein gp11
l: Short tail fiber protein gp12
m: Short tail fiber protein gp12
n: Short tail fiber protein gp12
o: Tail tube protein gp19
p: Tail tube protein gp19
q: Baseplate wedge protein gp25
r: Baseplate tail-tube protein gp48
s: Baseplate wedge protein gp53
t: Baseplate tail-tube protein gp54
u: Baseplate wedge protein gp6
v: Baseplate wedge protein gp6
w: Baseplate wedge protein gp7
x: Baseplate wedge protein gp8
y: Baseplate wedge protein gp8
z: Baseplate wedge protein gp9
AA: Baseplate wedge protein gp9
AB: Baseplate wedge protein gp9
AC: Baseplate wedge protein gp10
AD: Baseplate wedge protein gp10
AE: Baseplate wedge protein gp10
AF: Baseplate wedge protein gp11
AG: Baseplate wedge protein gp11
AH: Baseplate wedge protein gp11
AI: Short tail fiber protein gp12
AJ: Short tail fiber protein gp12
BA: Short tail fiber protein gp12
BB: Tail tube protein gp19
BC: Tail tube protein gp19
BD: Baseplate wedge protein gp25
BE: Baseplate tail-tube protein gp48
BF: Baseplate wedge protein gp53
BG: Baseplate tail-tube protein gp54
BH: Baseplate wedge protein gp6
BI: Baseplate wedge protein gp6
BJ: Baseplate wedge protein gp7
CA: Baseplate wedge protein gp8
CB: Baseplate wedge protein gp8
CC: Baseplate wedge protein gp9
CD: Baseplate wedge protein gp9
CE: Baseplate wedge protein gp9
CF: Baseplate wedge protein gp10
CG: Baseplate wedge protein gp10
CH: Baseplate wedge protein gp10
CI: Baseplate wedge protein gp11
CJ: Baseplate wedge protein gp11
DA: Baseplate wedge protein gp11
DB: Short tail fiber protein gp12
DC: Short tail fiber protein gp12
DD: Short tail fiber protein gp12
DE: Tail tube protein gp19
DF: Tail tube protein gp19
DG: Baseplate wedge protein gp25
DH: Baseplate tail-tube protein gp48
DI: Baseplate wedge protein gp53
DJ: Baseplate tail-tube protein gp54
EA: Baseplate wedge protein gp6
EB: Baseplate wedge protein gp6
EC: Baseplate wedge protein gp7
ED: Baseplate wedge protein gp8
EE: Baseplate wedge protein gp8
EF: Baseplate wedge protein gp9
EG: Baseplate wedge protein gp9
EH: Baseplate wedge protein gp9
EI: Baseplate wedge protein gp10
EJ: Baseplate wedge protein gp10
FA: Baseplate wedge protein gp10
FB: Baseplate wedge protein gp11
FC: Baseplate wedge protein gp11
FD: Baseplate wedge protein gp11
FE: Short tail fiber protein gp12
FF: Short tail fiber protein gp12
FG: Short tail fiber protein gp12
FH: Tail tube protein gp19
FI: Tail tube protein gp19
FJ: Baseplate wedge protein gp25
GA: Baseplate tail-tube protein gp48
GB: Baseplate wedge protein gp53
GC: Baseplate tail-tube protein gp54
GD: Baseplate wedge protein gp6
GE: Baseplate wedge protein gp6
GF: Baseplate wedge protein gp7
GG: Baseplate wedge protein gp8
GH: Baseplate wedge protein gp8
GI: Baseplate wedge protein gp9
GJ: Baseplate wedge protein gp9
HA: Baseplate wedge protein gp9
HB: Baseplate wedge protein gp10
HC: Baseplate wedge protein gp10
HD: Baseplate wedge protein gp10
HE: Baseplate wedge protein gp11
HF: Baseplate wedge protein gp11
HG: Baseplate wedge protein gp11
HH: Short tail fiber protein gp12
HI: Short tail fiber protein gp12
HJ: Short tail fiber protein gp12
IA: Tail tube protein gp19
IB: Tail tube protein gp19
IC: Baseplate wedge protein gp25
ID: Baseplate tail-tube protein gp48
IE: Baseplate wedge protein gp53
IF: Baseplate tail-tube protein gp54
YA: Peptidoglycan hydrolase gp5
YB: Peptidoglycan hydrolase gp5
YC: Peptidoglycan hydrolase gp5
YD: Baseplate hub protein gp27
YE: Baseplate hub protein gp27
YF: Baseplate hub protein gp27
ZA: Uncharacterized 10.2 kDa protein in segC-Gp6 intergenic region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,490,099152
Polymers6,489,651145
Non-polymers4487
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1577510 Å2
ΔGint-8354 kcal/mol
Surface area2099780 Å2
MethodPISA

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Components

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Baseplate wedge protein ... , 8 types, 96 molecules ABXYuvBHBIEAEBGDGECZwBJECGFDEabxyCACBEDEEGGGH...

#1: Protein
Baseplate wedge protein gp6 / Gene product 6 / gp6


Mass: 74492.641 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / Plasmid details: am18/am23 mutant / References: UniProt: P19060
#2: Protein
Baseplate wedge protein gp7 / Gene product 7 / gp7


Mass: 119336.516 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / Plasmid details: am18/am23 mutant / References: UniProt: P19061
#3: Protein
Baseplate wedge protein gp8 / Gene product 8 / gp8


Mass: 38041.668 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / Plasmid details: am18/am23 mutant / References: UniProt: P19062
#4: Protein
Baseplate wedge protein gp9 / Gene product 9 / gp9


Mass: 31024.725 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / Plasmid details: am18/am23 mutant / References: UniProt: P10927
#5: Protein
Baseplate wedge protein gp10 / Gene product 10 / gp10


Mass: 66281.680 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / Plasmid details: am18/am23 mutant / References: UniProt: P10928
#6: Protein
Baseplate wedge protein gp11 / Gene product 11 / gp11


Mass: 23725.523 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / Plasmid details: am18/am23 mutant / References: UniProt: P10929
#9: Protein
Baseplate wedge protein gp25 / Outer wedge of baseplate protein / Protein Gp25


Mass: 15111.101 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / Plasmid details: am18/am23 mutant / References: UniProt: P09425
#11: Protein
Baseplate wedge protein gp53 / Gene product 53 / gp53


Mass: 22990.885 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / Plasmid details: am18/am23 mutant / References: UniProt: P16011

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Protein , 5 types, 37 molecules OPQlmnAIAJBADBDCDDFEFFFGHHHIHJRSopBBBCDEDFFHFIIAIB...

#7: Protein
Short tail fiber protein gp12 / Gene product 12 / gp12


Mass: 56253.926 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / Plasmid details: am18/am23 mutant / References: UniProt: P10930
#8: Protein
Tail tube protein gp19 / Gene product 19 / gp19


Mass: 18479.613 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / Plasmid details: am18/am23 mutant / References: UniProt: P13333
#13: Protein Peptidoglycan hydrolase gp5 / Protein Gp5


Mass: 63183.723 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Details: The chain breaks in gp5 (chains YA, YB and YC) between residues 76 and 77 were introduced by the refinement program. The starting model did not contain these breaks. This region lies in the ...Details: The chain breaks in gp5 (chains YA, YB and YC) between residues 76 and 77 were introduced by the refinement program. The starting model did not contain these breaks. This region lies in the symmetry mismatched region of our map and cannot be refined reliably. The crystal structure of the gp5-gp27 complex - PDB code 1K28 - gives a more precise description of the polypeptide chain conformation at this location.
Source: (natural) Enterobacteria phage T4 (virus) / Plasmid details: am18/am23 mutant / References: UniProt: P16009, lysozyme
#14: Protein Baseplate hub protein gp27 / Gene product 27 / gp27 / Hub protein 27


Mass: 44431.062 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / Plasmid details: am18/am23 mutant / References: UniProt: P17172
#15: Protein Uncharacterized 10.2 kDa protein in segC-Gp6 intergenic region


Mass: 10233.663 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / Plasmid details: am18/am23 mutant / References: UniProt: P39234

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Baseplate tail-tube protein ... , 2 types, 12 molecules UrBEDHGAIDWtBGDJGCIF

#10: Protein
Baseplate tail-tube protein gp48 / Baseplate-tube cap / Gene product 48 / gp48


Mass: 39770.332 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / Plasmid details: am18/am23 mutant / References: UniProt: P13339
#12: Protein
Baseplate tail-tube protein gp54 / Gene product 54 / gp54


Mass: 35001.188 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / Plasmid details: am18/am23 mutant / References: UniProt: P13341

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Non-polymers , 2 types, 7 molecules

#16: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#17: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe

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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: Hexagonal pre-attachment T4 baseplate-tail tube complex
Type: COMPLEX
Details: Only the baseplate and the proximal part of the tail tube were selected for 3D reconstruction. The total mass of the reconstructed volume was approximately 6.5 MDa.
Entity ID: #1-#15 / Source: NATURAL
Molecular weightValue: 8.7 MDa / Experimental value: NO
Source (natural)Organism: Enterobacteria phage T4 (virus) / Strain: am18/am23 mutant
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTRIS-hydrochloride pH 8TRIS-HCl1
2100 mMsodium chlorideNaCl1
38 mMmagnesium sulfateMgSO41
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: In addition to hexagonal pre-attachment baseplate-tail tube complexes, the sample also contained some star-shaped, hubless post-attachment baseplates. The current model is the hexagonal pre- ...Details: In addition to hexagonal pre-attachment baseplate-tail tube complexes, the sample also contained some star-shaped, hubless post-attachment baseplates. The current model is the hexagonal pre-attachment baseplate-tail tube complex.
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %
Details: Applied 3.5 ul of sample and blotting 3 seconds before plunging

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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 / Nominal magnification: 105000 X / Calibrated magnification: 37700 X / Nominal defocus max: 4000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: HELIUM / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 80 K / Temperature (min): 80 K
Image recordingElectron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV
Image scansMovie frames/image: 40 / Used frames/image: 3-40

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Processing

EM software
IDNameVersionCategoryDetails
1EMAN2particle selectione2boxer.py
4CTFFIND4CTF correction
5RELION1.4CTF correction
8Coot0.8.2model fitting
10RELION1.4initial Euler assignment
11RELION1.4final Euler assignment
13RELION1.43D reconstruction
14PHENIX1.10.1-2155model refinementphenix.real_space_refine
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 47516
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 4.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37913 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-ID
13H2T

3h2t

1
21N7Z

1n7z

1
31S2E

1s2e

1
42FKK

2fkk

1
51EL6

1el6

1
61H6W

1h6w
PDB Unreleased entry

1
71OCY

1ocy

1
84HRZ

4hrz
PDB Unreleased entry

1
91K28

1k28

1
104KU0

4ku0

1

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