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- PDB-7efc: 1.70 A cryo-EM structure of streptavidin -

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Basic information

Entry
Database: PDB / ID: 7efc
Title1.70 A cryo-EM structure of streptavidin
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: 1.7 Å
AuthorsHiraizumi, M. / Yamashita, K. / Nishizawa, T. / Kotecha, A. / Nureki, O.
CitationJournal: To Be Published
Title: 1.70 A cryo-EM structure of streptavidin using all frames (corresponding to 70 e/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
  • EMDB-31083
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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
Molecular weightExperimental value: NO
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: 1.7 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: 1.7→76.255 Å / Cor.coef. Fo:Fc: 0.89 / WRfactor Rwork: 0.356 / SU B: 4.072 / SU ML: 0.104 / Average fsc overall: 0.6041 / Average fsc work: 0.6041 / ESU R: 0.049
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.3564 157319 -
all0.3564 --
obs--100 %
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 44.597 Å2
Baniso -1Baniso -2Baniso -3
1-0.017 Å2-0 Å2-0 Å2
2--0.037 Å2-0 Å2
3----0.054 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0270.012986
ELECTRON MICROSCOPYr_bond_other_d0.0260.018865
ELECTRON MICROSCOPYr_ext_dist_refined_d0.4090.11486
ELECTRON MICROSCOPYr_angle_refined_deg3.0221.6421350
ELECTRON MICROSCOPYr_angle_other_deg2.261.5781981
ELECTRON MICROSCOPYr_dihedral_angle_1_deg8.6642.023128
ELECTRON MICROSCOPYr_dihedral_angle_2_deg31.33922.17446
ELECTRON MICROSCOPYr_dihedral_angle_3_deg13.61315130
ELECTRON MICROSCOPYr_dihedral_angle_4_deg24.548154
ELECTRON MICROSCOPYr_chiral_restr0.030.2136
ELECTRON MICROSCOPYr_gen_planes_refined0.0010.021167
ELECTRON MICROSCOPYr_gen_planes_other00.02245
ELECTRON MICROSCOPYr_nbd_refined0.0510.2172
ELECTRON MICROSCOPYr_symmetry_nbd_other0.0490.21210
ELECTRON MICROSCOPYr_nbtor_refined0.0990.2674
ELECTRON MICROSCOPYr_symmetry_nbtor_other0.0380.2864
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.0270.2106
ELECTRON MICROSCOPYr_symmetry_nbd_refined0.0260.222
ELECTRON MICROSCOPYr_nbd_other0.0350.274
ELECTRON MICROSCOPYr_symmetry_xyhbond_nbd_refined0.0220.212
ELECTRON MICROSCOPYr_mcbond_it5.5464.479512
ELECTRON MICROSCOPYr_mcbond_other5.5524.474511
ELECTRON MICROSCOPYr_mcangle_it8.9726.718640
ELECTRON MICROSCOPYr_mcangle_other8.9666.725641
ELECTRON MICROSCOPYr_scbond_it5.9474.865474
ELECTRON MICROSCOPYr_scbond_other5.9414.868475
ELECTRON MICROSCOPYr_scangle_it9.3297.022710
ELECTRON MICROSCOPYr_scangle_other9.3227.024711
ELECTRON MICROSCOPYr_lrange_it24.549211.8722354
ELECTRON MICROSCOPYr_lrange_other24.773212.0192309
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 50 / % reflection obs: 100 %

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor Rwork
1.7-1.7170.76247210.76247210.0630.762
1.717-1.7350.67546180.67546180.0910.675
1.735-1.7530.64146870.64146870.070.641
1.753-1.7720.66645020.66645020.1030.666
1.772-1.7920.65445000.65445000.160.654
1.792-1.8120.59344310.59344310.1860.593
1.812-1.8330.57744720.57744720.2740.577
1.833-1.8550.60643170.60643170.2750.606
1.855-1.8770.6442680.6442680.310.64
1.877-1.9010.6241950.6241950.3710.62
1.901-1.9250.60141990.60141990.390.601
1.925-1.950.57341660.57341660.4160.573
1.95-1.9760.5341330.5341330.4780.53
1.976-2.0030.49740160.49740160.5110.497
2.003-2.0320.44839610.44839610.5910.448
2.032-2.0610.45339470.45339470.6460.453
2.061-2.0920.42338540.42338540.660.423
2.092-2.1250.39437750.39437750.6920.394
2.125-2.1590.40237440.40237440.7150.402
2.159-2.1940.40336810.40336810.7120.403
2.194-2.2320.39536320.39536320.7540.395
2.232-2.2710.38135610.38135610.7480.381
2.271-2.3130.36535410.36535410.8010.365
2.313-2.3570.35433480.35433480.8070.354
2.357-2.4040.3434240.3434240.8150.34
2.404-2.4530.35932810.35932810.820.359
2.453-2.5060.33832190.33832190.8430.338
2.506-2.5620.31231650.31231650.8570.312
2.562-2.6220.32531140.32531140.8660.325
2.622-2.6870.28829820.28829820.8860.288
2.687-2.7570.28230140.28230140.8990.282
2.757-2.8320.27828770.27828770.9160.278
2.832-2.9140.26627770.26627770.9250.266
2.914-3.0040.26326550.26326550.9230.263
3.004-3.1020.25526620.25526620.9260.255
3.102-3.2110.24225170.24225170.9420.242
3.211-3.3320.24324380.24324380.9420.243
3.332-3.4670.23423770.23423770.9420.234
3.467-3.6210.22822900.22822900.9490.228
3.621-3.7980.21421550.21421550.950.214
3.798-4.0020.22220690.22220690.9470.222
4.002-4.2440.24119440.24119440.9410.241
4.244-4.5370.22518130.22518130.950.225
4.537-4.8990.23517110.23517110.9430.235
4.899-5.3640.24715590.24715590.9330.247
5.364-5.9930.37114250.37114250.8740.371
5.993-6.9130.50112580.50112580.8360.501
6.913-8.450.55210600.55210600.790.552
8.45-11.8770.6018010.6018010.8390.601
11.877-76.2550.9144670.9144670.9130.914

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