3ERR: PDB entry 3ERR

Microtubule binding domain from mouse cytoplasmic dynein as a fusion with seryl-tRNA synthetase. Determined by X-ray diffraction at 2.27 Å resolution. Released 25 Nov 2008.

Method: X-ray diffraction
Resolution: 2.27 Å
Organisms: Mus musculus, Thermus thermophilus
Chains: 2
Atoms: 8,589
Mol. weight: 122.61 kDa
Ligands: AMP
Released: 25 Nov 2008

Explore 3ERR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3ERR contains 66 α-helices and 39 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 33 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5
α-helix	11-21	11
α-helix	27-3295	44
α-helix	3299-3306	8
α-helix	3313-3325	13
α-helix	3333-3336	4
α-helix	3339-3341	3
α-helix	3345-3351	7
α-helix	3354-3356	3
α-helix	3359-3364	6
α-helix	3365-3370	6
α-helix	3377-3383	7
α-helix	3387-98	46
α-helix	101-106	6
α-helix	114-116	3
β-strand	118-123	6	1
α-helix	133-135	3
α-helix	136-143	8
β-strand	146	1	2
α-helix	150-154	5
β-strand	161-162	2	2
α-helix	163-182	20
β-strand	186-189	4	1
β-strand	193-195	3	3
α-helix	196-202	7
α-helix	209-211	3
β-strand	214-215	2	3
β-strand	220-222	3	3
α-helix	227-233	7
β-strand	238-240	3	4
α-helix	241-243	3
α-helix	244	1
β-strand	246-255	10	1
β-strand	274-284	11	1
α-helix	288-308	21
β-strand	313-317	5	1
α-helix	318-319	2
β-strand	329-337	9	1
α-helix	338-340	3
β-strand	342-353	12	1
α-helix	355-360	6
β-strand	363-365	3	4
β-strand	371-373	3	4
α-helix	374	1
β-strand	375-384	10	1
α-helix	386-395	10
β-strand	396	1	5
β-strand	402-403	2	5
α-helix	404-405	2
α-helix	406-408	3
α-helix	409-412	4
β-strand	416-417	2	5

Chain B: 33 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	4-9	6
α-helix	13-21	9
α-helix	27-3295	44
α-helix	3300-3307	8
α-helix	3313-3325	13
α-helix	3333-3341	9
α-helix	3345-3351	7
α-helix	3354-3356	3
α-helix	3359-3364	6
α-helix	3365-3370	6
α-helix	3377-3380	4
α-helix	3387-98	46
α-helix	101-106	6
α-helix	110-111	2
α-helix	114-116	3
β-strand	118-123	6	2
α-helix	133-135	3
α-helix	136-143	8
β-strand	146	1	1
α-helix	150-154	5
β-strand	161-162	2	1
α-helix	163-182	20
α-helix	185	1
β-strand	186-189	4	2
β-strand	193-195	3	6
α-helix	196-202	7
α-helix	209-211	3
β-strand	213-214	2	6
β-strand	215	1	3
β-strand	220-222	3	6
α-helix	227-233	7
β-strand	238-240	3	7
α-helix	241-243	3
α-helix	244	1
β-strand	246-255	10	2
β-strand	274-284	11	2
α-helix	288-308	21
β-strand	313-317	5	2
α-helix	320-323	4
β-strand	329-337	9	2
α-helix	338-340	3
β-strand	342-351	10	2
α-helix	355-360	6
β-strand	363-365	3	7
β-strand	371-373	3	7
β-strand	375-384	10	2
α-helix	386-395	10
β-strand	396	1	8
β-strand	402-403	2	8
α-helix	406-408	3
α-helix	409-412	4
β-strand	416-417	2	8
α-helix	418-419	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
fusion protein of microtubule binding domain from mouse cytoplasmic dynein and seryl-tRNA…	A, B	protein	536	Mus musculus, Thermus thermophilus	Q5SJX7 (AlphaFold model), Q9JHU4

Sequence of entity 1 (A, B), FASTA

>3ERR_1 fusion protein of microtubule binding domain from mouse cytoplasmic dynein and seryl-tRNA synthetase from Thermus thermophilus (chains A, B)
MVDLKRLRQEPEVFHRAIREKGVALDLEALLAVDEQLHKQQEVIADKQMSVKEDLDKVEP
AVIEAQNAVKSIKKQHLVEVRSMANPPAAVKLALESIALLLGESTTDWKQIRSIIMRENF
IPTIVNFSAEEISDAIREKMKKNYMSNPSYNYEIVNRASLAAGPMVKWAIAQLNYADMLK
RVEPLRNELQKLEDDAKDNQQKLEALLLQVPLPPWPGAPVGGEEANREIKRVGGPPEFSF
PPLDHVALMEKNGWWEPRISQVSGSRSYALKGDLALYELALLRFAMDFMARRGFLPMTLP
SYAREKAFLGTGHFPAYRDQVWAIAETDLYLTGTAEVVLNALHSGEILPYEALPLRYAGY
APAFRSEAGSFGKDVRGLMRVHQFHKVEQYVLTEASLEASDRAFQELLENAEEILRLLEL
PYRLVEVATGDMGPGKWRQVDIEVYLPSEGRYRETHSCSALLDWQARRANLRYRDPEGRV
RYAYTLNNTALATPRILAMLLENHQLQDGRVRVPQALIPYMGKEVLEPGAHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
AMP	Adenosine monophosphate	C10 H14 N5 O7 P	2

Primary citation

Structure and functional role of dynein's microtubule-binding domain. Carter, A.P., Garbarino, J.E., Wilson-Kubalek, E.M. et al. Science (2008) 322:1691-1695. DOI 10.1126/science.1164424 · PubMed

Other PDB entries of the same protein (UniProt Q5SJX7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8FD6 2.9 Å, Engineered human dynein motor domain in the microtubule-unbound state in the buffer…
8FDT 3.2 Å, Engineered human dynein motor domain in the microtubule-unbound state with LIS1 complex…
8FDU 3.3 Å, Engineered human dynein motor domain in the microtubule-unbound state with LIS1 complex…
8FCY 3.4 Å, Engineered human dynein motor domain in microtubule-bound state

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