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- PDB-7efd: 1.77 A cryo-EM structure of Streptavidin using first 40 frames (c... -

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Basic information

Entry
Database: PDB / ID: 7efd
Title1.77 A cryo-EM structure of Streptavidin using first 40 frames (corresponding to about 40 e/A^2 total dose)
ComponentsStreptavidin
KeywordsCYTOSOLIC PROTEIN / STREPTAVIDIN
Function / homology
Function and homology information


biotin binding / extracellular region
Similarity search - Function
Avidin-like, conserved site / Avidin-like domain signature. / Avidin / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile.
Similarity search - Domain/homology
BIOTIN / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.77 Å
AuthorsHiraizumi, M. / Yamashita, K. / Nishizawa, T. / Kotecha, A. / Nureki, O.
CitationJournal: To Be Published
Title: 1.77 A cryo-EM structure of Streptavidin using first 40 frames (corresponding to about 40e/A^2 total dose)
Authors: Hiraizumi, M.
History
DepositionMar 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • Biological unit as complete point assembly
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0942
Polymers18,8501
Non-polymers2441
Water70339
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3768
Polymers75,3994
Non-polymers9774
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation3
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: D2 (2x2 fold dihedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(-1), (-1), (1)111.051, 111.051
3generate(1), (-1), (-1)111.051, 111.051
4generate(-1), (1), (-1)111.051, 111.051

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Components

#1: Protein Streptavidin


Mass: 18849.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces avidinii (bacteria) / References: UniProt: P22629
#2: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: Streptavidin / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Streptomyces avidinii (bacteria)
Buffer solutionpH: 7.2
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 70 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4053

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Processing

SoftwareName: REFMAC / Version: 5.8.0272 / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4.1.13CTF correction
7MOLREPmodel fitting
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
12RELION3.13D reconstruction
13REFMAC5.8.0272model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 1.77 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 153976 / Symmetry type: POINT
Atomic model buildingSpace: RECIPROCAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-ID
15N7X

5n7x

M5N7X1
21MK5

1mk5

A1MK52
RefinementResolution: 1.77→76.255 Å / Cor.coef. Fo:Fc: 0.895 / WRfactor Rwork: 0.349 / SU B: 3.828 / SU ML: 0.099 / Average fsc overall: 0.6978 / Average fsc work: 0.6978 / ESU R: 0.053
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.3492 139383 -
all0.3492 --
obs--100 %
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 45.492 Å2
Baniso -1Baniso -2Baniso -3
1--0.306 Å20 Å20 Å2
2--0.51 Å2-0 Å2
3----0.203 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0280.012986
ELECTRON MICROSCOPYr_bond_other_d0.0270.018865
ELECTRON MICROSCOPYr_ext_dist_refined_d0.410.11486
ELECTRON MICROSCOPYr_angle_refined_deg3.0231.6421350
ELECTRON MICROSCOPYr_angle_other_deg2.3081.5781981
ELECTRON MICROSCOPYr_dihedral_angle_1_deg8.6872.023128
ELECTRON MICROSCOPYr_dihedral_angle_2_deg31.922.17446
ELECTRON MICROSCOPYr_dihedral_angle_3_deg14.66415130
ELECTRON MICROSCOPYr_dihedral_angle_4_deg24.663154
ELECTRON MICROSCOPYr_chiral_restr0.030.2136
ELECTRON MICROSCOPYr_gen_planes_refined0.0010.021167
ELECTRON MICROSCOPYr_gen_planes_other00.02245
ELECTRON MICROSCOPYr_nbd_refined0.0550.2170
ELECTRON MICROSCOPYr_symmetry_nbd_other0.050.21242
ELECTRON MICROSCOPYr_nbtor_refined0.10.2694
ELECTRON MICROSCOPYr_symmetry_nbtor_other0.040.2906
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.0280.2108
ELECTRON MICROSCOPYr_symmetry_nbd_refined0.020.222
ELECTRON MICROSCOPYr_nbd_other0.040.270
ELECTRON MICROSCOPYr_symmetry_xyhbond_nbd_refined0.0280.212
ELECTRON MICROSCOPYr_mcbond_it6.3094.482512
ELECTRON MICROSCOPYr_mcbond_other6.314.478511
ELECTRON MICROSCOPYr_mcangle_it9.9776.722640
ELECTRON MICROSCOPYr_mcangle_other9.9726.728641
ELECTRON MICROSCOPYr_scbond_it7.115.014474
ELECTRON MICROSCOPYr_scbond_other7.1025.018475
ELECTRON MICROSCOPYr_scangle_it10.927.194710
ELECTRON MICROSCOPYr_scangle_other10.9137.197711
ELECTRON MICROSCOPYr_lrange_it26.566214.5052364
ELECTRON MICROSCOPYr_lrange_other26.775214.092320
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 40 / % reflection obs: 100 %

Resolution (Å)Rfactor RworkNum. reflection RworkNum. reflection allFsc workRfactor allWRfactor Rwork
1.77-1.793523652360.202
1.793-1.8160.719518851880.2370.7190.719
1.816-1.840.649493949390.3430.6490.649
1.84-1.8660.663504650460.3550.6630.663
1.866-1.8920.657495649560.4090.6570.657
1.892-1.920.597483348330.4390.5970.597
1.92-1.9490.597471647160.4690.5970.597
1.949-1.9790.527478547850.5210.5270.527
1.979-2.010.476462746270.6150.4760.476
2.01-2.0440.458452145210.6480.4580.458
2.044-2.0790.448448444840.6730.4480.448
2.079-2.1150.424444844480.7070.4240.424
2.115-2.1540.403425942590.7330.4030.403
2.154-2.1950.41427742770.7420.410.41
2.195-2.2390.388416841680.7840.3880.388
2.239-2.2850.382405540550.780.3820.382
2.285-2.3340.388401940190.8160.3880.388
2.334-2.3860.349396939690.8350.3490.349
2.386-2.4420.35379637960.8390.350.35
2.442-2.5030.335376537650.8540.3350.335
2.503-2.5670.321361636160.8630.3210.321
2.567-2.6380.326353035300.8730.3260.326
2.638-2.7140.296349034900.8850.2960.296
2.714-2.7980.285333833380.9090.2850.285
2.798-2.8890.277332733270.9210.2770.277
2.889-2.990.272313231320.9260.2720.272
2.99-3.1030.253299329930.9330.2530.253
3.103-3.230.235288928890.9420.2350.235
3.23-3.3730.25287328730.9370.250.25
3.373-3.5370.244263426340.9420.2440.244
3.537-3.7280.229254725470.9460.2290.229
3.728-3.9540.225240924090.9430.2250.225
3.954-4.2260.253228322830.940.2530.253
4.226-4.5630.237209220920.9490.2370.237
4.563-4.9970.257193519350.9410.2570.257
4.997-5.5840.284176117610.9150.2840.284
5.584-6.4420.443155115510.8430.4430.443
6.442-7.8760.536129212920.8180.5360.536
7.876-11.0790.445103410340.8470.4450.445
11.079-76.2550.7285665660.9110.7280.728

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