PDB-6tbn: Crystal structure of CIAO1-CIAO2B CIA core complex

ID or keywords:

Entry

Database: PDB / ID: 6tbn

Title

Crystal structure of CIAO1-CIAO2B CIA core complex

Components

MIP18 family protein galla-2
Probable cytosolic iron-sulfur protein assembly protein Ciao1

Keywords

BIOSYNTHETIC PROTEIN / Fe-S cluster / Fe-S / CIA / CIA core complex

Function / homology

Function and homology information

cytosolic [4Fe-4S] assembly targeting complex / protein maturation by [4Fe-4S] cluster transfer /

iron-sulfur cluster assembly /

chromosome segregation /

cell division
Similarity search - Function

Biological species

Drosophila melanogaster (fruit fly)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Kassube, S.A. / Thoma, N.H.

Funding support

Switzerland, 3items

Citation

Journal: Nat Struct Mol Biol / Year: 2020
Title: Structural insights into Fe-S protein biogenesis by the CIA targeting complex.
Authors: Susanne A Kassube / Nicolas H Thomä /

Abstract: The cytosolic iron-sulfur (Fe-S) assembly (CIA) pathway is required for the insertion of Fe-S clusters into cytosolic and nuclear client proteins, including many DNA replication and repair factors. ...

History

Deposition	Nov 1, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 29, 2020	Provider: repository / Type: Initial release
Revision 1.1	Feb 10, 2021	Group: Database references / Category: citation Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Jan 24, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6tbn.cif.gz	343.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6tbn.ent.gz	237.5 KB	Display	PDB format
PDBx/mmJSON format	6tbn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tb/6tbn ftp://data.pdbj.org/pub/pdb/validation_reports/tb/6tbn	HTTPS FTP

-
Related structure data

Related structure data	11016C 11017C 11018C 11019C 11020C 11021C 6tblC 6tc0C 3fm0S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3uoz-1 3uoz-2 4xhu-1 4c77-d 3uoy-2 4c74-d 6y48-3 6yjq-2 3uoy-1 4aos-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: MIP18 family protein galla-2

B: Probable cytosolic iron-sulfur protein assembly protein Ciao1

hetero molecules

55.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	125.580, 125.580, 85.490
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	79
Space group name H-M	I4
Space group name Hall	I4
Symmetry operation	#1: x,y,z #2: -y,x,z #3: y,-x,z #4: -x,-y,z #5: x+1/2,y+1/2,z+1/2 #6: -y+1/2,x+1/2,z+1/2 #7: y+1/2,-x+1/2,z+1/2 #8: -x+1/2,-y+1/2,z+1/2

#1: Protein	MIP18 family protein galla-2 Mass: 17822.127 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: galla-2, CG7949 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9VTC4
#2: Protein	Probable cytosolic iron-sulfur protein assembly protein Ciao1 Mass: 37283.277 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Ciao1, CG12797 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q7K1Y4
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 3.06 Å³/Da / Density % sol: 59.78 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 8.5, 25% PEG MME 2k

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 7, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2→19.86 Å / Num. obs: 44669 / % possible obs: 99.38 % / Redundancy: 53.9 % / B_iso Wilson estimate: 39.64 Å² / CC_1/2: 0.998 / Net I/σ(I): 14.8
Reflection shell	Resolution: 2→2.071 Å / Mean I/σ(I) obs: 0.72 / Num. unique obs: 4240 / CC_1/2: 0.142

-
Processing

Software

Name	Version	Classification
PHENIX	1.16_3549	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3FM0

3fm0

Resolution: 2→19.86 Å / SU ML: 0.2624 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.1731
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2084	2229	4.99 %
R_work	0.1805	42407	-
obs	0.1819	44636	99.45 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 53.22 Å²

Refinement step

Cycle: LAST / Resolution: 2→19.86 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3740	0	1	149	3890

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0062	3863
X-RAY DIFFRACTION	f_angle_d	0.7035	5265
X-RAY DIFFRACTION	f_chiral_restr	0.299	591
X-RAY DIFFRACTION	f_plane_restr	0.0043	683
X-RAY DIFFRACTION	f_dihedral_angle_d	16.1066	2296

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2-2.04	0.3739	126	0.3695	2408	X-RAY DIFFRACTION	91.45
2.04-2.09	0.3064	139	0.3247	2666	X-RAY DIFFRACTION	100
2.09-2.14	0.341	145	0.3056	2677	X-RAY DIFFRACTION	99.96
2.14-2.2	0.3307	133	0.3111	2628	X-RAY DIFFRACTION	99.96
2.2-2.27	0.2763	139	0.2765	2642	X-RAY DIFFRACTION	100
2.27-2.34	0.2632	141	0.256	2665	X-RAY DIFFRACTION	100
2.34-2.42	0.2635	139	0.2368	2645	X-RAY DIFFRACTION	100
2.42-2.52	0.2344	141	0.2252	2675	X-RAY DIFFRACTION	100
2.52-2.63	0.2752	138	0.217	2631	X-RAY DIFFRACTION	99.96
2.63-2.77	0.2623	140	0.1989	2667	X-RAY DIFFRACTION	100
2.77-2.94	0.2275	141	0.2001	2668	X-RAY DIFFRACTION	100
2.94-3.17	0.2565	141	0.2001	2684	X-RAY DIFFRACTION	100
3.17-3.49	0.1944	140	0.1721	2650	X-RAY DIFFRACTION	100
3.49-3.99	0.1914	140	0.1477	2675	X-RAY DIFFRACTION	100
3.99-5.01	0.1403	142	0.1129	2691	X-RAY DIFFRACTION	100
5.01-19.86	0.1526	144	0.1371	2735	X-RAY DIFFRACTION	99.9

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	1.10567427666	2.45863572078	-0.789642001979	7.39358765258	-2.40411409995	0.822935894382	0.208277392085	-0.424431676357	-0.573008534377	0.497967160812	0.35335046969	-0.884398234614	0.788301079414	0.635824005435	0.237847079929	0.656446186728	0.0789723535917	-0.0634893783163	0.470255353831	-0.0109697166904	0.614455529936	27.3447829354	132.138715587	36.1875439243
2	0.95747046545	1.01649474514	-1.19267509671	2.78640188988	-1.32438045045	1.47975802661	-0.432059949644	-0.250149909631	1.34904032906	0.0148546214075	0.991722522577	-0.887686382349	-0.412519049302	0.602012708782	0.323753237955	0.692042199102	0.107800130364	-0.0849822945583	0.989613628737	-0.296618877948	1.24556371985	32.9977733431	125.997672302	21.4633713051
3	3.43366868741	-0.579268631668	1.51669463535	3.63741670384	0.127042894582	4.5675494634	-0.077028218588	0.707972567187	-0.229614995621	-0.647257251192	-0.00330673199066	0.458214137204	0.210699542279	-0.143952816525	-0.150264329936	0.41583333494	0.0977384256913	-0.058083035209	0.471834559985	-0.0644574811975	0.459046763196	10.5688755331	106.520697252	14.9388153226
4	3.10899203189	-0.184000035883	0.802192269687	2.42944431801	0.226466866803	2.35542004532	0.037962066972	0.451932855048	0.312252999118	-0.389703860886	-0.125697680735	0.121096270179	-0.17408090218	-0.112266554416	0.0834167486476	0.321047312951	0.0379349732577	-0.0292862770839	0.304214233523	-0.00291806326417	0.358598399827	12.8325047931	114.521926724	20.0611985368
5	2.6679231678	-0.813344937463	0.701971929659	1.42917163819	-0.0257966191361	2.04886060064	0.0436100536579	-0.23277313872	-0.186471063194	0.068028669783	0.00569880307621	0.128405390817	0.0884374578493	-0.196678026757	-0.0928436229348	0.273225556779	0.0359960814969	-0.01873166628	0.262281926364	-0.00470574042341	0.349614848546	12.7669059859	106.066666962	28.6978507447
6	6.39610550866	-1.18350078873	0.844967611487	4.71567609673	-2.12514662674	6.04651415154	0.490976075883	0.967849402085	-0.771033675272	-0.292551162691	0.124871731837	-0.395832416904	1.14705872204	0.380710503256	-0.316677278082	0.53668971422	0.0674134372115	-0.0975609863904	0.407189558415	-0.1059887577	0.720429279292	14.1438492461	94.0247100637	20.4820300338
7	2.62867473813	0.451142200972	-0.00342471826351	2.63801724087	-0.54369892371	1.71920270362	-0.140636971298	0.130175695541	0.468028999805	-0.0119856641348	-0.177346392806	-0.325602002786	-0.317880190221	0.693575395437	0.312513122788	0.318712224671	-0.0495519414583	-0.0529461819362	0.455613828665	0.0678540413732	0.473526195849	40.928335212	107.783277647	41.3429731794
8	2.26564267674	-1.3114687482	0.830549982494	3.66400841616	-0.750439137592	4.65327327375	-0.412380784718	0.178675919801	0.125026482543	-0.284808974474	0.016354692824	-0.650100627423	0.0845938594649	0.501986178871	0.162364769731	0.321329832356	0.0389515475895	0.0129283940097	0.485152365746	0.0777070025404	0.482929958491	41.7469812131	98.0979541726	40.1026867527
9	3.10216503129	0.192666643887	0.912985992479	2.17086009294	-0.884057016837	3.58818794909	0.150695151624	0.00879497571271	-0.23040250359	-0.0609809127371	-0.0763226053023	-0.180663551219	0.48927545167	0.375540185986	-0.0178889239794	0.306538652837	0.079925526645	-0.0232676204228	0.326506289592	0.0208384826335	0.364649642385	36.1785801756	92.0554958373	45.1596760166
10	2.32593797875	-0.775318388395	0.985530540758	2.03876724402	-1.4697099626	2.8187364284	0.0229589571578	-0.351907818685	-0.325043864728	0.0200198638733	0.199206645172	0.138369712821	0.211874033804	-0.270461054883	-0.193618184454	0.277452380699	0.00470937198349	-0.0236556519333	0.401493387313	0.0638747000777	0.343315750989	23.9099973878	93.0079595991	52.6572138508
11	2.07333022025	-0.398215374141	0.563810530154	1.99118601325	-0.527479057543	2.31974988844	-0.285779016804	-0.684069150045	0.192487433366	0.682891206277	0.250989704403	0.0381824283747	-0.722415986614	-0.542776606026	0.0432943061635	0.526206492683	0.191836582779	-0.0281488973925	0.623445722739	-0.0499886587611	0.35097956311	20.1137450488	110.448325125	58.215977206
12	2.95547299415	-0.253958512825	0.288942261502	2.13594781847	-0.684445029281	2.64836145894	-0.188142194426	-0.210041756163	0.599997244482	0.343204051335	-0.0604671099722	-0.368625826979	-0.691968708625	0.0854416481153	0.260997295445	0.473663127197	-0.00409409338318	-0.147606901789	0.36232911924	-0.0374308832758	0.491630660322	34.7175692377	116.080142889	46.4798892784

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 9 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 10 through 35 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 36 through 53 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 54 through 79 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 80 through 141 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 142 through 155 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 0 through 27 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 28 through 46 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 47 through 92 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 93 through 156 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 157 through 254 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 255 through 335 )

-
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