PDB-4rfx: Crystal Structure of the Dynactin DCTN1 Fragment involved in Dyne...

ID or keywords:

Entry

Database: PDB / ID: 4rfx

Title

Crystal Structure of the Dynactin DCTN1 Fragment involved in Dynein Interaction

Components

Dynactin subunit 1

Keywords

PROTEIN TRANSPORT / Coiled-coil / Dynein Intermediate Chain

Function / homology

Function and homology information

cell cortex region / positive regulation of intracellular protein transport / microtubule plus-end / dynein complex / microtubule associated complex / nuclear migration / establishment of mitotic spindle orientation / cytoplasmic microtubule organization / centriole / regulation of mitotic spindle organization ...
Similarity search - Function

Biological species

Gallus gallus (chicken)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.9 Å

Authors

Findeisen, P. / Eckert, C. / Kollmar, M.

Citation

Journal: To be Published
Title: Crystal Structure of the Dynactin DCTN1 Fragment involved in Dynein Interaction
Authors: Findeisen, P. / Eckert, C. / Kollmar, M.

History

Deposition	Sep 29, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 7, 2015	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Refinement description / Category: software
Revision 1.2	Nov 6, 2019	Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary Category: entity_name_com / entity_src_gen ...entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif Item: _entity_name_com.name / _entity_src_gen.gene_src_common_name ..._entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4rfx.cif.gz	214.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4rfx.ent.gz	177.1 KB	Display	PDB format
PDBx/mmJSON format	4rfx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4rfx_validation.pdf.gz	462 KB	Display	wwPDB validaton report
Full document	4rfx_full_validation.pdf.gz	474.8 KB	Display
Data in XML	4rfx_validation.xml.gz	18.9 KB	Display
Data in CIF	4rfx_validation.cif.gz	26.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rf/4rfx ftp://data.pdbj.org/pub/pdb/validation_reports/rf/4rfx	HTTPS FTP

-
Related structure data

Similar structure data	6jfv-2 3u59-3 6bl7-d 4ytd-d 6ys4-3 1d7m-d 6ys4-1 6jfv-1 3u59-1 3u1c-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Dynactin subunit 1

B: Dynactin subunit 1

C: Dynactin subunit 1

D: Dynactin subunit 1

E: Dynactin subunit 1

82 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Dynactin subunit 1

B: Dynactin subunit 1

defined by author&software
32.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Dynactin subunit 1

D: Dynactin subunit 1

defined by author&software
32.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Dynactin subunit 1

defined by author&software
32.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	155.320, 155.320, 129.260
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLU	GLU	GLN	GLN	A	A	434 - 530	42 - 138
2	1	GLU	GLU	GLN	GLN	B	B	434 - 530	42 - 138
1	2	MET	MET	GLN	GLN	A	A	432 - 530	40 - 138
2	2	MET	MET	GLN	GLN	C	C	432 - 530	40 - 138
1	3	VAL	VAL	GLN	GLN	A	A	433 - 530	41 - 138
2	3	VAL	VAL	GLN	GLN	D	D	433 - 530	41 - 138
1	4	LEU	LEU	SER	SER	A	A	436 - 529	44 - 137
2	4	LEU	LEU	SER	SER	E	E	436 - 529	44 - 137
1	5	GLU	GLU	GLN	GLN	B	B	434 - 530	42 - 138
2	5	GLU	GLU	GLN	GLN	C	C	434 - 530	42 - 138
1	6	GLU	GLU	GLN	GLN	B	B	434 - 530	42 - 138
2	6	GLU	GLU	GLN	GLN	D	D	434 - 530	42 - 138
1	7	LEU	LEU	SER	SER	B	B	436 - 529	44 - 137
2	7	LEU	LEU	SER	SER	E	E	436 - 529	44 - 137
1	8	VAL	VAL	GLN	GLN	C	C	433 - 530	41 - 138
2	8	VAL	VAL	GLN	GLN	D	D	433 - 530	41 - 138
1	9	LEU	LEU	SER	SER	C	C	436 - 529	44 - 137
2	9	LEU	LEU	SER	SER	E	E	436 - 529	44 - 137
1	10	LEU	LEU	SER	SER	D	D	436 - 529	44 - 137
2	10	LEU	LEU	SER	SER	E	E	436 - 529	44 - 137

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10

#1: Protein	Dynactin subunit 1 / 150 kDa dynein-associated polypeptide / DAP-150 / DP-150 / p150-glued Mass: 16408.918 Da / Num. of mol.: 5 Fragment: COILED_COIL 1 DOMAIN, UNP residues RESIDUES 412-533 Mutation: L419V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: DCTN1 / Plasmid: pRSFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)RIL / References: UniProt: P35458

#1: Protein

Dynactin subunit 1 / 150 kDa dynein-associated polypeptide / DAP-150 / DP-150 / p150-glued

Mass: 16408.918 Da / Num. of mol.: 5
Fragment: COILED_COIL 1 DOMAIN, UNP residues RESIDUES 412-533
Mutation: L419V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Gallus gallus (chicken) / Gene: DCTN1 / Plasmid: pRSFDuet-1 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)RIL / References: UniProt: P35458

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal	Density Matthews: 4.75 Å³/Da / Density % sol: 74.11 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M Na-citrate pH 5.5, 5% PEG 4000, 0.1 M ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	SLS	X10SA	1	0.979
SYNCHROTRON	SLS	X10SA	2	1.033

Detector

Type	ID	Detector	Date
DECTRIS PILATUS 6M	1	PIXEL	Feb 24, 2012
DECTRIS PILATUS 6M	2	PIXEL	Dec 19, 2013

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	double-crystal Si(111)	MAD	M	x-ray	1
2	double crystal	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.979	1
2	1.033	1

Reflection

Resolution: 2.9→49.7 Å / Num. all: 35602 / Num. obs: 35585 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 26.3 %

Reflection shell

Resolution: 2.9→2.95 Å / Redundancy: 27.2 % / Num. unique all: 1725 / % possible all: 99.88

-
Processing

Software

Name	Version	Classification
SHELXD		phasing
REFMAC	5.7.0029	refinement
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.9→49.7 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.934 / SU B: 38.029 / SU ML: 0.295 / Cross valid method: THROUGHOUT / σ(I): 1.78 / ESU R: 0.382 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27705	1733	5 %	RANDOM
R_work	0.25841	-	-	-
obs	0.25935	32808	96.89 %	-
all	-	35649	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 108.667 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.6 Å²	-0 Å²	-0 Å²
2-	-	-4.6 Å²	-0 Å²
3-	-	-	9.19 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→49.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4065	0	0	0	4065

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.019	4075
X-RAY DIFFRACTION	r_bond_other_d	0.009	0.02	3937
X-RAY DIFFRACTION	r_angle_refined_deg	1.623	1.979	5470
X-RAY DIFFRACTION	r_angle_other_deg	1.649	3	9030
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.59	5	489
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.714	25.577	260
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.846	15	843
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.756	15	50
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	626
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	4691
X-RAY DIFFRACTION	r_gen_planes_other	0.006	0.02	877
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	4476	0.22
1	2	B	4476	0.22
2	1	A	4628	0.21
2	2	C	4628	0.21
3	1	A	4729	0.19
3	2	D	4729	0.19
4	1	A	4353	0.22
4	2	E	4353	0.22
5	1	B	4615	0.2
5	2	C	4615	0.2
6	1	B	4647	0.2
6	2	D	4647	0.2
7	1	B	4311	0.23
7	2	E	4311	0.23
8	1	C	4682	0.2
8	2	D	4682	0.2
9	1	C	4393	0.23
9	2	E	4393	0.23
10	1	D	4394	0.22
10	2	E	4394	0.22

LS refinement shell

Resolution: 2.9→2.975 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.457	84	-
R_work	0.477	1623	-
obs	-	-	66.29 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.3523	-1.0016	0.1487	4.4591	-0.5771	0.2281	-0.2505	-0.1647	0.0097	-0.1181	0.445	-0.0868	0.0043	-0.1177	-0.1945	0.53	0.0904	-0.0087	0.2108	0.0214	0.2389	117.6489	0.9442	23.2794
2	0.5824	-1.8385	0.2637	6.7153	-0.8702	0.1298	-0.2287	-0.1203	-0.0658	0.4647	0.2651	0.079	-0.0585	-0.0579	-0.0365	0.5498	0.0656	0.0438	0.2757	-0.0238	0.0478	117.8224	1.7182	23.4564
3	5.7618	-1.356	0.5024	0.4267	-0.1127	0.0799	0.1998	0.1599	-0.0593	-0.0319	-0.1377	0.0329	0.0664	0.0381	-0.062	0.2598	0.0677	-0.0559	0.5338	-0.0455	0.0851	18.3168	114.3497	42.0873
4	6.4296	-1.1505	0.3397	0.2759	-0.0705	0.0289	0.0738	-0.0059	0.0545	0.0051	-0.0664	0.0184	0.0563	0.016	-0.0074	0.3191	0.0408	-0.0094	0.5575	-0.0427	0.0131	16.2676	114.9161	42.4547
5	3.6803	-3.6395	-0.2766	3.6421	0.2214	0.1641	-0.0414	-0.231	0.0007	-0.076	0.155	0.0329	0.0881	0.0232	-0.1136	0.388	0.1468	0.0096	0.3548	-0.074	0.137	80.215	75.8722	33.2693

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	432 - 531
2	X-RAY DIFFRACTION	2	B	434 - 531
3	X-RAY DIFFRACTION	3	C	431 - 531
4	X-RAY DIFFRACTION	4	D	433 - 532
5	X-RAY DIFFRACTION	5	E	436 - 530

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi