9dnb

CryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1.

Method: ELECTRON MICROSCOPY D_max: 174.8 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Dynein heavy chain, cytoplasmic

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1219–4092	Not recorded	Nuclear distribution protein PAC1 × 2 （P39946） ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 8；50 mM TrisHCl [pH 8.0], 150 mM KOAc, 2 mM MgOAc, 1mM EGTA, 1 mM DTT cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9DNB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3QMZ Crystal structure of the cytoplasmic dynein heavy chain motor domain Deposited 2011-02-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1364–4092（2729 aa） Fragment：unp residues 1364-4092	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；277 K；16% PEG3350, 0.1 M sodium citrate, 0.2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 5.7	Resolution 6.00 Å R-free 0.430
3QMZ Crystal structure of the cytoplasmic dynein heavy chain motor domain Deposited 2011-02-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1364–4092（2729 aa） Fragment：unp residues 1364-4092	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；277 K；16% PEG3350, 0.1 M sodium citrate, 0.2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 5.7	Resolution 6.00 Å R-free 0.430
4AI6 Dynein Motor Domain - ADP complex Deposited 2012-02-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1364–3038（1675 aa） Fragment：RESIDUES 1-218,1364-3038,3292-4092 Chain A 3292–4092（801 aa） Fragment：RESIDUES 1-218,1364-3038,3292-4092 Chain B 1364–3038（1675 aa） Fragment：RESIDUES 1-218,1364-3038,3292-4092 Chain B 3292–4092（801 aa） Fragment：RESIDUES 1-218,1364-3038,3292-4092	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 4 SO4 SULFATE ION × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.40 Å R-free 0.303
4AKG Dynein Motor Domain - ATP complex Deposited 2012-02-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1364–3038（1675 aa） Fragment：RESIDUES 1-218,1364-3038,3292-4092 Chain A 3292–4092（801 aa） Fragment：RESIDUES 1-218,1364-3038,3292-4092 Chain B 1364–3038（1675 aa） Fragment：RESIDUES 1-218,1364-3038,3292-4092 Chain B 3292–4092（801 aa） Fragment：RESIDUES 1-218,1364-3038,3292-4092	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 SO4 SULFATE ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.30 Å R-free 0.305
4AKH Dynein Motor Domain - AMPPNP complex Deposited 2012-02-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1364–3038（1675 aa） Fragment：RESIDUES 1-218,1364-3038,3292-4092 Chain A 3292–4092（801 aa） Fragment：RESIDUES 1-218,1364-3038,3292-4092	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 SO4 SULFATE ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.60 Å R-free 0.302
4AKH Dynein Motor Domain - AMPPNP complex Deposited 2012-02-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1364–3038（1675 aa） Fragment：RESIDUES 1-218,1364-3038,3292-4092 Chain B 3292–4092（801 aa） Fragment：RESIDUES 1-218,1364-3038,3292-4092	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 SO4 SULFATE ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.60 Å R-free 0.302
4AKI Dynein Motor Domain - LuAc derivative Deposited 2012-02-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1364–3038（1675 aa） Fragment：RESIDUES 1-218,1364-3038,3292-4092 Chain A 3292–4092（801 aa） Fragment：RESIDUES 1-218,1364-3038,3292-4092 Chain B 1364–3038（1675 aa） Fragment：RESIDUES 1-218,1364-3038,3292-4092 Chain B 3292–4092（801 aa） Fragment：RESIDUES 1-218,1364-3038,3292-4092	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 SO4 SULFATE ION × 6 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.70 Å R-free 0.289
4W8F Crystal structure of the dynein motor domain in the AMPPNP-bound state Deposited 2014-08-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1364–3038（1675 aa） Chain A 3292–4092（801 aa）	Mutation：E1849Q Mutation：E1849Q	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；4-10% PEG 3350 and 200-300 mM NaAc	Resolution 3.54 Å R-free 0.262
4W8F Crystal structure of the dynein motor domain in the AMPPNP-bound state Deposited 2014-08-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1364–3038（1675 aa） Chain B 3292–4092（801 aa）	Mutation：E1849Q Mutation：E1849Q	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；4-10% PEG 3350 and 200-300 mM NaAc	Resolution 3.54 Å R-free 0.262
4W8F Crystal structure of the dynein motor domain in the AMPPNP-bound state Deposited 2014-08-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1364–3038（1675 aa） Chain A 3292–4092（801 aa） Chain B 1364–3038（1675 aa） Chain B 3292–4092（801 aa）	Mutation：E1849Q Mutation：E1849Q Mutation：E1849Q Mutation：E1849Q	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 8 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；4-10% PEG 3350 and 200-300 mM NaAc	Resolution 3.54 Å R-free 0.262
5AFR N-terminal fragment of dynein heavy chain Deposited 2015-01-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–557（557 aa） Fragment：N-TERMINAL FRAGMENT OF TAIL DOMAIN, RESIDUES 1-557 Chain B 1–557（557 aa） Fragment：N-TERMINAL FRAGMENT OF TAIL DOMAIN, RESIDUES 1-557	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 5.00 Å R-free 0.437
5VH9 Cryo-EM structure of yeast cytoplasmic dynein-1 with Lis1 and ATP Deposited 2017-04-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1448–3028（1581 aa） Fragment：UNP residues 1448-3028,3298-4092 Chain A 3298–4092（795 aa） Fragment：UNP residues 1448-3028,3298-4092	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.70 Å
5VLJ Cryo-EM structure of yeast cytoplasmic dynein with Walker B mutation at AAA3 in presence of ATP-VO4 Deposited 2017-04-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1448–3028（1581 aa） Fragment：UNP residues 1448-3028,3298-4092 Chain A 3298–4092（795 aa） Fragment：UNP residues 1448-3028,3298-4092	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 10.50 Å
6KIO Complex of yeast cytoplasmic dynein MTBD-High and MT without DTT Deposited 2019-07-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain M 3095–3224（130 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.94 Å
6KIQ Complex of yeast cytoplasmic dynein MTBD-High and MT with DTT Deposited 2019-07-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain M 3095–3224（130 aa）	Mutation：I3101C, V3222C	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8；DTT was added to the final concentration of 1 mM. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.62 Å
6KJN The microtubule-binding domains of yeast cytoplasmic dynein in the high affinity state Deposited 2019-07-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3095–3232（138 aa）	Mutation：I3101C, V3222C	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 200；Pressure 1 NMR sample composition 0.75 mM [U-99% 13C; U-99% 15N] Cytoplasmic dynein, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.75 mM [U-99% 13C; U-99% 15N] Cytoplasmic dynein, 100% D2O \| 100% D2O	Resolution not provided
6KJO The microtubule-binding domains of yeast cytoplasmic dynein in the low affinity state Deposited 2019-07-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3095–3232（138 aa） Fragment：The microtubule-binding domain	Mutation：S3097C, V3222C	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 200；Pressure 1 NMR sample composition 1.0 mM [U-99% 13C; U-99% 15N] The microtubule-binding domain of cytoplasmic dynein, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1.0 mM [U-99% 13C; U-99% 15N] The microtubule-binding domain of cytoplasmic dynein, 100% D2O \| 100% D2O	Resolution not provided
7MI1 X-ray structure of yeast dynein motor domain in the presence of a pyrazolo-pyrimidinone-based compound (compound 20) Deposited 2021-04-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1364–3038（1675 aa） Chain A 3292–4092（801 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；100 mM Bis-Tris pH 6.9, 200 mM sodium acetate, 12% PEG 3350, and 10 mM TCEP	Resolution 4.50 Å R-free 0.320
7MI3 Signal subtracted reconstruction of AAA2, AAA3, and AAA4 domains of dynein in the presence of a pyrazolo-pyrimidinone-based compound, Model 4 Deposited 2021-04-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1364–3038（1675 aa） Chain A 3292–4092（801 aa）	Not recorded	ZG7 (8S)-6-(3-bromophenoxy)-2-[1-(4-chlorophenyl)cyclopropyl]-7-hydroxypyrazolo[1,5-a]pyrimidine-3-carbonitrile × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
7MI6 Yeast dynein motor domain in the presence of a pyrazolo-pyrimidinone-based compound, Model 1 Deposited 2021-04-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1364–3038（1675 aa） Chain A 3292–4092（801 aa）	Mutation：E1849Q Mutation：E1849Q	ZG7 (8S)-6-(3-bromophenoxy)-2-[1-(4-chlorophenyl)cyclopropyl]-7-hydroxypyrazolo[1,5-a]pyrimidine-3-carbonitrile × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
7MI8 Signal subtracted reconstruction of AAA5 and AAA6 domains of dynein in the presence of a pyrazolo-pyrimidinone-based compound, Model 5 Deposited 2021-04-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1364–3038（1675 aa） Chain A 3292–4092（801 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
9DI3 CryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1. Deposited 2024-09-05	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1219–4092（2874 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM TrisHCl [pH 8.0], 150 mM KOAc, 2 mM MgOAc, 1mM EGTA, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
9DIU CryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1. Deposited 2024-09-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1219–4092（2874 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM Tris [pH 8.0], 150 mM KOAc, 2 mM MgOAc, 1mM EGTA, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
9DJ7 CryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1. Deposited 2024-09-06	Different construct Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1218–4092（2875 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM TrisHCl [pH 8.0], 150 mM KOAc, 2 mM MgOAc, 1mM EGTA, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
9DJU CryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1. Deposited 2024-09-06	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1219–4092（2874 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM TrisHCl [pH 8.0], 150 mM KOAc, 2 mM MgOAc, 1mM EGTA, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
9DJY CryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1. Deposited 2024-09-07	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1219–4092（2874 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM TrisHCl [pH 8.0], 150 mM KOAc, 2 mM MgOAc, 1mM EGTA, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9DJZ CryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1. Deposited 2024-09-07	Different construct Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1218–4092（2875 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM TrisHCl [pH 8.0], 150 mM KOAc, 2 mM MgOAc, 1mM EGTA, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
9DK0 CryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1. Deposited 2024-09-07	Different construct Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1218–4092（2875 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM TrisHCl [pH 8.0], 150 mM KOAc, 2 mM MgOAc, 1mM EGTA, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
9DKD CryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1. Deposited 2024-09-08	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1219–4092（2874 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM TrisHCl [pH 8.0], 150 mM KOAc, 2 mM MgOAc, 1mM EGTA, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9DKE CryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1. Deposited 2024-09-08	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1219–4092（2874 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM TrisHCl [pH 8.0], 150 mM KOAc, 2 mM MgOAc, 1mM EGTA, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9DKH CryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1. Deposited 2024-09-08	Different construct Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1218–4092（2875 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM TrisHCl [pH 8.0], 150 mM KOAc, 2 mM MgOAc, 1mM EGTA, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
9DKJ CryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1. Deposited 2024-09-09	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1218–4092（2875 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM TrisHCl [pH 8.0], 150 mM KOAc, 2 mM MgOAc, 1mM EGTA, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
9DKM CryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1. Deposited 2024-09-09	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1219–4092（2874 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM Tris [pH 8.0], 150 mM KOAc, 2 mM MgOAc, 1mM EGTA, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9DKX CryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1. Deposited 2024-09-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1219–4092（2874 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
9DLD CryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1. Deposited 2024-09-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1219–4092（2874 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9DLE CryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1. Deposited 2024-09-10	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1219–4092（2874 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM TrisHCl [pH 8.0], 150 mM KOAc, 2 mM MgOAc, 1mM EGTA, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9DMW CryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1. Deposited 2024-09-16	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1219–4092（2874 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM TrisHCl [pH 8.0], 150 mM KOAc, 2 mM MgOAc, 1mM EGTA, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
9DN5 CryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1. Deposited 2024-09-16	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1219–4092（2874 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM TrisHCl [pH 8.0], 150 mM KOAc, 2 mM MgOAc, 1mM EGTA, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9DN7 CryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1. Deposited 2024-09-16	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1219–4092（2874 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM TrisHCl [pH 8.0], 150 mM KOAc, 2 mM MgOAc, 1mM EGTA, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.25 Å
9MFV Motor domain with Apo AAA1 and ADP AAA3 from yeast full-length dynein-1 in 0.1 mM ATP condition Deposited 2024-12-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–4092（4092 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9MFW Motor domain with ADP AAA1 and ADP AAA3 from yeast full-length dynein-1 in 0.1 mM ATP condition Deposited 2024-12-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–4092（4092 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
9MFX Motor domain alone with Apo AAA1 and ADP AAA3 from yeast full-length dynein-1 and Pac1 in 0.1 mM ATP condition Deposited 2024-12-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–4092（4092 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9MFY Motor domain-Pac1 complex with ADP AAA1 and Apo AAA3 from yeast full-length dynein-1 and Pac1 in 0.1 mM ATP condition Deposited 2024-12-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–4092（4092 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å

39 other PDB entries and 43 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DYHC_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–2875； UniProt 1219–4092

Nuclear distribution protein PAC1

Saccharomyces cerevisiae

UniProt P39946

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 1–494 Chain C； UniProt 1–494	Not recorded	Dynein heavy chain, cytoplasmic × 1 （P36022） ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 8；50 mM TrisHCl [pH 8.0], 150 mM KOAc, 2 mM MgOAc, 1mM EGTA, 1 mM DTT cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.00 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9DNB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7MGM Structure of yeast cytoplasmic dynein with AAA3 Walker B mutation bound to Lis1 Deposited 2021-04-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–494（494 aa） Chain C 1–494（494 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8DZZ Cryo-EM structure of chi dynein bound to Lis1 Deposited 2022-08-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 1–494（494 aa） Chain C 1–494（494 aa） Chain E 1–494（494 aa） Chain F 1–494（494 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
8E00 Symmetry expansion of yeast cytoplasmic dynein-1 bound to Lis1 in the chi conformation. Deposited 2022-08-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–494（494 aa） Chain C 1–494（494 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9DJ7 CryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1. Deposited 2024-09-06	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–494（494 aa） Chain C 1–494（494 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM TrisHCl [pH 8.0], 150 mM KOAc, 2 mM MgOAc, 1mM EGTA, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
9DJU CryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1. Deposited 2024-09-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–494（494 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM TrisHCl [pH 8.0], 150 mM KOAc, 2 mM MgOAc, 1mM EGTA, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
9DJZ CryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1. Deposited 2024-09-07	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–494（494 aa） Chain C 1–494（494 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM TrisHCl [pH 8.0], 150 mM KOAc, 2 mM MgOAc, 1mM EGTA, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
9DK0 CryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1. Deposited 2024-09-07	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–494（494 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM TrisHCl [pH 8.0], 150 mM KOAc, 2 mM MgOAc, 1mM EGTA, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
9DKH CryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1. Deposited 2024-09-08	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–494（494 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM TrisHCl [pH 8.0], 150 mM KOAc, 2 mM MgOAc, 1mM EGTA, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
9DKM CryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1. Deposited 2024-09-09	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–494（494 aa） Chain C 1–494（494 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM Tris [pH 8.0], 150 mM KOAc, 2 mM MgOAc, 1mM EGTA, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9DKX CryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1. Deposited 2024-09-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–494（494 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
9DLD CryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1. Deposited 2024-09-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–494（494 aa） Chain C 1–494（494 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9DLE CryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1. Deposited 2024-09-10	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–494（494 aa） Chain C 1–494（494 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM TrisHCl [pH 8.0], 150 mM KOAc, 2 mM MgOAc, 1mM EGTA, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9DMW CryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1. Deposited 2024-09-16	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–494（494 aa） Chain C 1–494（494 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM TrisHCl [pH 8.0], 150 mM KOAc, 2 mM MgOAc, 1mM EGTA, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
9DN5 CryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1. Deposited 2024-09-16	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–494（494 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM TrisHCl [pH 8.0], 150 mM KOAc, 2 mM MgOAc, 1mM EGTA, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9DN7 CryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1. Deposited 2024-09-16	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–494（494 aa） Chain C 1–494（494 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8；50 mM TrisHCl [pH 8.0], 150 mM KOAc, 2 mM MgOAc, 1mM EGTA, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.25 Å
9MFY Motor domain-Pac1 complex with ADP AAA1 and Apo AAA3 from yeast full-length dynein-1 and Pac1 in 0.1 mM ATP condition Deposited 2024-12-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–494（494 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å

16 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LIS1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–495； UniProt 1–494 Author chain C； PDBConstruct 2–495； UniProt 1–494

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9dnb
Deposition date deposition_date	2024-09-17
Structure title title	CryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1.
Keywords keywords	Enzyme, AAA protein, MOTOR PROTEIN; MOTOR PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	51.58 Å
Radius of gyration Rg (electron density) rg_electron	51.07 Å
Forward intensity I(0) i0	1490980000.00
Molecular weight molecular_weight	325380.0 kDa
Excluded volume excluded_volume	407880 Å³
Envelope volume envelope_volume	581040 Å³
Hydration-shell volume shell_volume	92466 Å³
Envelope diameter envelope_diameter	179.1 Å
Shell Rg shell_rg	56.21 Å
Envelope Rg envelope_rg	50.79 Å
Shape Rg shape_rg	51.14 Å
Total Rg total_rg	50.96 Å
Total atoms total_atoms	22963
Residues n_residues	3020
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	174.8 Å
Rg (real space) rg_real	51.59 Å
Rg uncertainty (real space) rg_real_error	1.46 Å
I(0) (real space) i0_real	1.4910e+09
I(0) uncertainty (real space) i0_real_error	2.7690e+07
Rg (reciprocal space) rg_reciprocal	51.55 Å
I(0) (reciprocal space) i0_reciprocal	1491000000.0000
Solution quality estimate total_estimate	0.8763
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	62.0 Å
Skewness Skewness skewness	0.345
Kurtosis Kurtosis kurtosis	-0.348
Angular range angular_range	— – 0.1550 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	185500000.0000
Real-space data points n_real_points	32
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.867; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.796

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Dynein heavy chain, cytoplasmic
Molecular weight formula_weight	331525.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	22963

GDQLTHVVEEVKTYDLVWRSIKNLWEDVQRTFETPWCRVDVLLLQSDLANFLRRADELPRAVKQFEMYKSLFSQVNMLTSVNKILVELKDGALKPRHWNMIFRDIGKRQIQKNLLDKLEFSLKDVMVLNLTLNEILLTKIIERAQKEFVIEKSLNRIKKFWKEAQYEVIEHSSGLKLVREWDVLEQACKEDLEELVSMKASNYYKIFEQDCLDLESKLTKLSEIQVNWVEVQFYWLDLYGILGENLDIQNFLPLETSKFKSLTSEYKMITTRAFQLDTTIEVIHIPNFDTTLKLTIDSLKMIKSSLSTFLERQRRQFPRFYFLGNDDLLKIIGSGKHHDQVSKFMKKMFGSIESIIFFEDSITGVRSVEGEVLNLNEKIELKDSIQAQEWLNILDTEIKLSVFTQFRDCLGQLKDGTDIEVVVSKYIFQAILLSAQVMWTELVEKCLQTNEFSKYWKEVDMKIKGLLDKLNKSSDNVKKKIEALLVEYLHFNNVIGQLKNCSTKEEARLLWAKVQKFYQKNDTLDDLNSVFISQSGYLLQYKFEYIGIPERLIYTPLLLVGFATLTDSLHQKYGGCFFGPAGTGKTETVKAFGQNLGRVVVVFNCDDSFDYQVLSRLLVGITQIGAWGCFDEFNRLDEKVLSAVSANIQQIQNGLQVGKSHITLLEEETPLSPHTAVFITLNPGYNGRSELPENLKKSFREFSMKSPQSGTIAEMILQIMGFEDSKSLASKIVHFLELLSSKCSSMNHYHFGLRTLKGVLRNCSPLVSEFGEGEKTVVESLKRVILPSLGDTDELVFKDELSKIFDSAGTPLNSKAIVQCLKDAGQRSGFSMSEEFLKKCMQFYYMQKTQQALILVGKAGCGKTATWKTVIDAMAIFDGHANVVYVIDTKVLTKESLYGSMLKATLEWRDGLFTSILRRVNDDITGTFKNSRIWVVFDSDLDPEYVEAMNSVLDDNKILTLPNGERLPIPPNFRILFETDNLDHTTPATITRCGLLWFSTDVCSISSKIDHLLNKSYEALDNKLSMFELDKLKDLISDSFDMASLTNIFTCSNDLVHILGVRTFNKLETAVQLAVHLISSYRQWFQNLDDKSLKDVITLLIKRSLLYALAGDSTGESQRAFIQTINTYFGHDSQELSDYSTIVIANDKLSFSSFCSEIPSVSLEAHEVMRPDIVIPTIDTIKHEKIFYDLLNSKRGIILCGPPGSGKTMIMNNALRNSSLYDVVGINFSKDTTTEHILSALHRHTNYVTTSKGLTLLPKSDIKNLVLFCDEINLPKLDKYGSQNVVLFLRQLMEKQGFWKTPENKWVTIERIHIVGACNPPTDPGRIPMSERFTRHAAILYLGYPSGKSLSQIYEIYYKAIFKLVPEFRSYTEPFARASVHLYNECKARYSTGLQSHYLFSPRELTRLVRGVYTAINTGPRQTLRSLIRLWAYEAWRIFADRLVGVKEKNSFEQLLYETVDKYLPNQDLGNISSTSLLFSGLLSLDFKEVNKTDLVNFIEERFKTFCDEELEVPMVIHESMVDHILRIDRALKQVQGHMMLIGASRTGKTILTRFVAWLNGLKIVQPKIHRHSNLSDFDMILKKAISDCSLKESRTCLIIDESNILETAFLERMNTLLANADIPDLFQGEEYDKLLNNLRNKTRSLGLLLDTEQELYDWFVGEIAKNLHVVFTICDPTNNKSSAMISSPALFNRCIINWMGDWDTKTMSQVANNMVDVVPMEFTDFIVPEVNKELVFTEPIQTIRDAVVNILIHFDRNFYQKMKVGVNPRSPGYFIDGLRALVKLVTAKYQDLQENQRFVNVGLEKLNESVLKVNELNKTLSKKSTELTEKEKEARSTLDKMLMEQNESERKQEATEEIKKILKVQEEDIRKRKEVVMKSIQDIEPTILEAQRGVKNIKKQQLTEIRSMVNPPSGVKIVMEAVCAILGYQFSNWRDIQQFIRKDDFIHNIVHYDTTLHMKPQIRKYMEEEFLSDPNFTYETINRASKACGPLYQWVNAQINFSKVLENVDPLRQEMKRIEFESLKTKANLLAAEEMTQDLEASIEVSKQKYSLLIRDVEAIKTEMSNVQANLDRSISLVKSLTFEKERWLNTTKQFSKTSQELIGNCIISSIYETYFGHLNERERGDMLVILKRLLGKFAVKYDVNYRFIDYLVTLDEKMKWLECGLDKNDYFLENMSIVMNSQDAVPFLLDPSSHMITVISNYYGNKTVLLSFLEEGFVKRLENAVRFGSVVIIQDGEFFDPIISRLISREFNHAGNRVTVEIGDHEVDVSGDFKLFIHSCDPSGDIPIFLRSRVRLVHFVTNKESIETRIFDITLTEENAEMQRKREDLIKLNTEYRLKLKNLEKRLLEELNNSQGNMLENDELMVTLNNLKKEAMNIEKKLSESEEFFPQFDNLVEEYSIIGKHSVKIFSMLEKFGQFHWFYGISIGQFLSCFKRVFIKKSRETRAARTRVDEILWLLYQEVYCQFSTALDKKFKMIMAMTMFCLYKFDIESEQYKEAVLTMIGVLSESSDGVPKLTVDTNDDLRYLWDYVTTKSYISALNWFKNEFFVDEWNIADVVANSENNYFTMASERDVDGTFKLIELAKASKESLKIIPLGSIENLNYAQEEISKSKIEGGWILLQNIQMSLSWVKTYLHKHVEETKAAEEHEKFKMFMTCHLTGDKLPAPLLQRTDRVVYEDIPGILDTVKDLWGSQFFTGKISGVWSVYCTFLLSWFHALITARTRLVPHGFSKKYYFNDCDFQFASVYLENVLATNSTNNIPWAQVRDHIATIVYGGKIDEEKDLEVVAKLCAHVFCGSDNLQIVPGVRIPQPLLQQSEEEERARLTAILSNTIEPADSLSSWLQLPRESILDYERLQAKEVASSTEQLLQEM

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;brewer's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Saccharomyces cerevisiae

Entity 2 Entity 2 polymer

Description description	Nuclear distribution protein PAC1
Molecular weight formula_weight	57030.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,C

GMTNWQQQLPLTDTQKNELDKSVLRYLNWNYKQTVRHEHAQDYESVRHAIVTLSGFLLQESVDRQEFISNNDTSNESMVDIDELLLPKKWNSIVRLQKKIIELEQNTETLVSQIKDLNTQVSELAQFKPTTSNGTSAHNVLKWIPRNLPSCLINVESSVTSVKLHPNLPIVFVATDHGKLYAFDLFNYTIPLASLQSHTKAITSMDVLFTNYTNSSKKNYLVIVTASKDLQIHVFKWVSEECKFQQIRSLLGHEHIVSAVKIWQKNNDVHIASCSRDQTVKIWDFHNGWSLKTFQPHSQWVRSIDVLGDYIISGSHDTTLRLTHWPSGNGLSVGTGHEFPIEKVKFIHFIEDSPEIRFRTPSTDRYKNWGMQYCVSASRDRTIKIWEIPLPTLMAHRAPIPNPTDSNFRCVLTLKGHLSWVRDISIRGQYLFSCADDKSVRCWDLNTGQCLHVWEKLHTGFVNCLDLDVDFDSNVTPRQMMVTGGLDCKSNVFMR

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;brewer's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Saccharomyces cerevisiae

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.00 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	67155

fit	/app/data/saxs_computation/dn/9dnb/9dnb.fit
pddf	/app/data/pr_computation/dn/9dnb/9dnb.pr.out
profile	/app/data/saxs_computation/dn/9dnb/9dnb.dat

CryoEM structures of yeast cytoplasmic dynein in the presence of ATP and Lis1.

1. Protein Identity and Related Structures Protein Identity & Related Structures

Dynein heavy chain, cytoplasmic

State in the Current Structure

Other States of the Same Protein in the Database

Nuclear distribution protein PAC1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)