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- PDB-5m6s: folding intermediate of spectrin R16 -

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Basic information

Entry
Database: PDB / ID: 5m6s
Titlefolding intermediate of spectrin R16
Descriptorspectrin
KeywordsSTRUCTURAL PROTEIN / spectrin / r16
Specimen sourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
MethodElectron microscopy (4.8 Å resolution / Particle / Single particle)
AuthorsNilsson, O.B. / Nickson, A.A. / Clarke, J.
CitationNat. Struct. Mol. Biol., 2017, 24, 221-225

Nat. Struct. Mol. Biol., 2017, 24, 221-225 StrPapers
Cotranslational folding of spectrin domains via partially structured states.
Ola B Nilsson / Adrian A Nickson / Jeffrey J Hollins / Stephan Wickles / Annette Steward / Roland Beckmann / Gunnar von Heijne / Jane Clarke

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 25, 2016 / Release: Jan 11, 2017
RevisionDateData content typeGroupProviderType
1.0Jan 11, 2017Structure modelrepositoryInitial release
1.1Jan 25, 2017Structure modelDatabase references
1.2Feb 1, 2017Structure modelDatabase references
1.3Mar 15, 2017Structure modelDatabase references

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Assembly

Deposited unit
A: spectrin


Theoretical massNumber of molelcules
Total (without water)19,3711
Polyers19,3711
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)0
ΔGint (kcal/M)0
Surface area (Å2)6420
MethodPISA

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Components

#1: Polypeptide(L)spectrin


Mass: 19370.596 Da / Num. of mol.: 1
Source: (gene. exp.) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

Biological process

Cellular component

Molecular function

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: spectrin folding intermediate bound to 70s ribosome / Type: RIBOSOME / Entity ID: 1 / Source: MULTIPLE SOURCES
Molecular weightValue: 2.5 deg. / Units: MEGADALTONS / Experimental flag: NO
Source (natural)Organism: Escherichia coli
Source (recombinant)Organism: Escherichia coli
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R3/3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 2.4 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameCategoryImaging IDImage processing ID
2EMTOOLSIMAGE ACQUISITION1
4CTFFIND4CTF CORRECTION1
9SPIDERINITIAL EULER ASSIGNMENT1
10SPIDERFINAL EULER ASSIGNMENT1
11SPIDERCLASSIFICATION1
12SPIDERRECONSTRUCTION1
CTF correctionType: NONE
3D reconstructionResolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 46067
Details: To exclude potential overfitting, the data were processed using a frequency limited refinement protocol by truncating high frequencies (low-pass filter at 8 A)
Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT

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