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- PDB-7dy0: 1.93 A cryo-EM structure of streptavidin -

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Basic information

Entry
Database: PDB / ID: 7dy0
Title1.93 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
Biological speciesStreptomyces avidinii (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.93 Å
AuthorsHiraizumi, M. / Yamashita, K. / Nishizawa, T. / Kikkawa, M. / Nureki, O.
CitationJournal: To Be Published
Title: 1.93 A cryo-EM structure of streptavidin
Authors: Hiraizumi, M.
History
DepositionJan 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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 / refine
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 / _refine.ls_d_res_high / _refine.ls_d_res_low

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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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  • Superimposition on EM map
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  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Streptavidin


Theoretical massNumber of molelcules
Total (without water)18,8501
Polymers18,8501
Non-polymers00
Water54030
1
A: Streptavidin

A: Streptavidin

A: Streptavidin

A: Streptavidin


Theoretical massNumber of molelcules
Total (without water)75,3994
Polymers75,3994
Non-polymers00
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)87.99963, 87.99963
3generate(1), (-1), (-1)87.99963, 87.99963
4generate(-1), (1), (-1)87.99963, 87.99963

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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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
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: coated grid with pentylamine before glow discharge / Grid 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 recordingAverage exposure time: 1.5 sec. / Electron dose: 70 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2277
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 15 eV

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Processing

SoftwareName: REFMAC / Version: 5.8.0272 / Classification: refinement
EM software
IDNameVersionCategory
1RELION3.1particle selection
2SerialEMimage acquisition
4CTFFIND4.1.13CTF correction
7MOLREPmodel fitting
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
12RELION3.13D reconstruction
19REFMAC5.8.0272model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 1.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19045 / Symmetry type: POINT
Atomic model buildingSpace: RECIPROCAL
Atomic model buildingPDB-ID: 5N7X

5n7x


Pdb chain-ID: M / Accession code: 5N7X / Source name: PDB / Type: experimental model
RefinementResolution: 1.93→1.93 Å / Cor.coef. Fo:Fc: 0.814 / WRfactor Rwork: 0.349 / SU B: 6.443 / SU ML: 0.146 / Average fsc overall: 0.6654 / Average fsc work: 0.6654 / ESU R: 0.077
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.3489 74239 -
all0.349 --
obs--100 %
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 49.861 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å2-0 Å2
2--0.308 Å20 Å2
3----0.167 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0120.012913
ELECTRON MICROSCOPYr_bond_other_d0.0020.018803
ELECTRON MICROSCOPYr_angle_refined_deg1.6961.6411249
ELECTRON MICROSCOPYr_angle_other_deg1.4461.5781834
ELECTRON MICROSCOPYr_dihedral_angle_1_deg8.2445118
ELECTRON MICROSCOPYr_dihedral_angle_2_deg27.79222.38142
ELECTRON MICROSCOPYr_dihedral_angle_3_deg15.77715124
ELECTRON MICROSCOPYr_dihedral_angle_4_deg24.32154
ELECTRON MICROSCOPYr_chiral_restr0.090.2125
ELECTRON MICROSCOPYr_gen_planes_refined0.0090.021073
ELECTRON MICROSCOPYr_gen_planes_other0.0020.02231
ELECTRON MICROSCOPYr_nbd_refined0.1660.2270
ELECTRON MICROSCOPYr_symmetry_nbd_other0.1780.21416
ELECTRON MICROSCOPYr_nbtor_refined0.1690.2876
ELECTRON MICROSCOPYr_symmetry_nbtor_other0.080.2986
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.1180.268
ELECTRON MICROSCOPYr_symmetry_nbd_refined0.2180.210
ELECTRON MICROSCOPYr_nbd_other0.1810.256
ELECTRON MICROSCOPYr_symmetry_xyhbond_nbd_refined0.1660.210
ELECTRON MICROSCOPYr_mcbond_it5.2575.067475
ELECTRON MICROSCOPYr_mcbond_other5.2625.054474
ELECTRON MICROSCOPYr_mcangle_it9.0317.59592
ELECTRON MICROSCOPYr_mcangle_other9.0257.605593
ELECTRON MICROSCOPYr_scbond_it5.5195.48438
ELECTRON MICROSCOPYr_scbond_other5.5135.502439
ELECTRON MICROSCOPYr_scangle_it9.3377.922657
ELECTRON MICROSCOPYr_scangle_other9.337.943658
ELECTRON MICROSCOPYr_lrange_it18.08494.0794104
ELECTRON MICROSCOPYr_lrange_other18.07193.9384096
LS refinement shell

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

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor Rwork
1.92-1.930.5410560.5410560.1480.54
1.93-1.940.56311640.56311640.210.563
1.94-1.9490.54610760.54610760.2360.546
1.949-1.960.55211260.55211260.2240.552
1.96-1.970.6049920.6049920.2150.604
1.97-1.980.60611030.60611030.2640.606
1.98-1.9910.58111480.58111480.2520.581
1.991-2.0020.59710350.59710350.2160.597
2.002-2.0130.5610680.5610680.2740.56
2.013-2.0240.54710630.54710630.3620.547
2.024-2.0350.55610480.55610480.2590.556
2.035-2.0470.50910350.50910350.3540.509
2.047-2.0580.52510300.52510300.3050.525
2.058-2.070.56410650.56410650.3230.564
2.07-2.0820.55810180.55810180.3490.558
2.082-2.0950.47210290.47210290.5250.472
2.095-2.1070.51110330.51110330.3470.511
2.107-2.120.5339440.5339440.50.533
2.12-2.1330.47310150.47310150.5120.473
2.133-2.1460.50910460.50910460.5360.509
2.146-2.160.5129820.5129820.5110.512
2.16-2.1740.5349970.5349970.5310.534
2.174-2.1880.54710010.54710010.5260.547
2.188-2.2020.4639610.4639610.5420.463
2.202-2.2170.4729440.4729440.6260.472
2.217-2.2320.4879520.4879520.5840.487
2.232-2.2470.46810030.46810030.6340.468
2.247-2.2620.4889510.4889510.5770.488
2.262-2.2780.5159230.5159230.5270.515
2.278-2.2940.488980.488980.5930.48
2.294-2.3110.4579300.4579300.6270.457
2.311-2.3280.4279680.4279680.6570.427
2.328-2.3450.4548790.4548790.6380.454
2.345-2.3630.4758900.4758900.6540.475
2.363-2.3810.4559260.4559260.6190.455
2.381-2.40.4228700.4228700.7120.422
2.4-2.4180.4558980.4558980.6770.455
2.418-2.4380.4069330.4069330.7180.406
2.438-2.4580.4068360.4068360.7450.406
2.458-2.4780.4148300.4148300.7580.414
2.478-2.4990.3559000.3559000.7810.355
2.499-2.520.3538510.3538510.750.353
2.52-2.5420.3788720.3788720.7630.378
2.542-2.5650.3618000.3618000.8140.361
2.565-2.5880.3488160.3488160.8180.348
2.588-2.6120.3558420.3558420.8050.355
2.612-2.6360.3318200.3318200.8280.331
2.636-2.6620.327810.327810.8360.32
2.662-2.6880.3557960.3557960.8270.355
2.688-2.7140.3358260.3358260.8330.335
2.714-2.7420.2967530.2967530.8750.296
2.742-2.770.37890.37890.8810.3
2.77-2.7990.3397730.3397730.8470.339
2.799-2.830.2887580.2887580.9010.288
2.83-2.8610.277230.277230.9070.27
2.861-2.8930.2817650.2817650.9130.281
2.893-2.9260.267470.267470.9160.26
2.926-2.9610.2347090.2347090.9480.234
2.961-2.9970.2497220.2497220.9370.249
2.997-3.0340.2397070.2397070.950.239
3.034-3.0730.2487120.2487120.9410.248
3.073-3.1130.2416740.2416740.940.241
3.113-3.1540.2326800.2326800.9380.232
3.154-3.1980.2466950.2466950.9440.246
3.198-3.2430.2296750.2296750.940.229
3.243-3.290.2426210.2426210.9450.242
3.29-3.340.2326590.2326590.950.232
3.34-3.3910.2716160.2716160.9410.271
3.391-3.4450.2316600.2316600.9480.231
3.445-3.5020.2215720.2215720.9560.221
3.502-3.5620.2436370.2436370.9560.243
3.562-3.6250.2125490.2125490.9590.212
3.625-3.6910.2166290.2166290.9550.216
3.691-3.7610.2035690.2035690.9660.203
3.761-3.8350.2025310.2025310.960.202
3.835-3.9140.2115970.2115970.9630.211
3.914-3.9980.1955030.1955030.9690.195
3.998-4.0880.2525430.2525430.9480.252
4.088-4.1840.2195350.2195350.960.219
4.184-4.2860.2364900.2364900.9630.236
4.286-4.3970.2154860.2154860.9630.215
4.397-4.5170.2285080.2285080.9580.228
4.517-4.6480.2054370.2054370.9680.205
4.648-4.790.1874600.1874600.9690.187
4.79-4.9460.1894470.1894470.9620.189
4.946-5.1190.1954160.1954160.9580.195
5.119-5.3110.2264290.2264290.9390.226
5.311-5.5270.2753860.2753860.930.275
5.527-5.7710.3094000.3094000.9290.309
5.771-6.050.3813310.3813310.9070.381
6.05-6.3740.3523500.3523500.8750.352
6.374-6.7570.3173190.3173190.9190.317
6.757-7.2190.4663060.4663060.8770.466
7.219-7.790.4153000.4153000.8530.415
7.79-8.5220.5152510.5152510.8490.515
8.522-9.510.5592350.5592350.8760.559
9.51-10.9450.6282150.6282150.8840.628
10.945-13.3190.6131790.6131790.9260.613
13.319-18.4850.9311400.9311400.9240.931
18.485-681.736801.736800.9891.736

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