PDB-6ra9: Novel structural features and post-translational modifications in...

ID or keywords:

Entry

Database: PDB / ID: 6ra9

Title

Novel structural features and post-translational modifications in eukaryotic elongation factor 1A2 from Oryctolagus cuniculus

Components

(Elongation factor 1-alpha ...) x 2

Keywords

TRANSLATION /

Moonlighting protein /

RNA binding protein /

posttranslational modifications /

protein binding /

oncoprotein

Function / homology

Function and homology information

translation elongation factor activity /

GTPase activity / GTP binding /

nucleus
Similarity search - Function

Biological species

Oryctolagus cuniculus (rabbit)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Carriles, A.A. / Hermoso, J. / Gago, F.

Funding support

Spain, 1items

Citation

Journal: Chembiochem / Year: 2021
Title: Structural Cues for Understanding eEF1A2 Moonlighting.
Authors: Carriles, A.A. / Mills, A. / Munoz-Alonso, M.J. / Gutierrez, D. / Dominguez, J.M. / Hermoso, J.A. / Gago, F.

History

Deposition	Apr 5, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 3, 2020	Provider: repository / Type: Initial release
Revision 1.1	Apr 7, 2021	Group: Database references / Category: citation / citation_author 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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Jan 24, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6ra9.cif.gz	443.2 KB	Display	PDBx/mmCIF format
PDB format	pdb6ra9.ent.gz	306.7 KB	Display	PDB format
PDBx/mmJSON format	6ra9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ra/6ra9 ftp://data.pdbj.org/pub/pdb/validation_reports/ra/6ra9	HTTPS FTP

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Related structure data

Related structure data	4c0sS S: Starting model for refinement
Similar structure data	4c0s-d 5vh4-d 5xp8-d 1kp5-3 6nb5-d 1uiv-d 6vav-d 4bo4-d 6vc4-d 3o78-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
Experimental dataset #1	Data reference: 10.1093/nar/gku974 / Data set type: other data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#81 - Sep 2006 Elongation Factors similarity (10) #121 - Jan 2010 70S Ribosomes similarity (10) #157 - Jan 2013 Transfer-Messenger RNA similarity (10) #104 - Aug 2008 Selenocysteine Synthase similarity (6) #245 - May 2020 Spliceosomes similarity (5)

Deposited unit

A: Elongation factor 1-alpha 2

B: Elongation factor 1-alpha 2

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: mass spectrometry

Unit cell

Length a, b, c (Å)	133.520, 133.520, 305.440
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	178
Space group name H-M	P6₁22
Space group name Hall	P6₁2(x,y,z+5/12)

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Elongation factor 1-alpha ... , 2 types, 2 molecules AB

#1: Protein	Elongation factor 1-alpha 2 / EF-1-alpha-2 / Eukaryotic elongation factor 1 A-2 / eEF1A-2 / Statin-S1 Mass: 49768.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: Q71V39
#2: Protein	Elongation factor 1-alpha 2 / EF-1-alpha-2 / Eukaryotic elongation factor 1 A-2 / eEF1A-2 / Statin-S1 Mass: 50415.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: Q71V39

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Non-polymers , 5 types, 139 molecules

#3: Chemical	ChemComp-GPE / L-ALPHA-GLYCEROPHOSPHORYLETHANOLAMINE Mass: 215.142 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₅H₁₄NO₆P
#4: Chemical	ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₁P₂ / Comment: GDP, energy-carrying molecule*YM
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO₄
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.92 Å³/Da / Density % sol: 68.6 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 50 mM Na citrate pH 5/MES pH 5.6, 2.2-2.6 M ammonium sulphate, 10 mM Mg acetate

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Data collection

Diffraction

Mean temperature: 80 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ALBA

/ Beamline: XALOC / Wavelength: 0.97926 Å

Detector

Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 17, 2015

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97926 Å / Relative weight: 1

Reflection

Resolution: 2.7→61.17 Å / Num. obs: 83606 / % possible obs: 100 % / Redundancy: 13 % / B_iso Wilson estimate: 60.78 Å² / CC_1/2: 0.995 / R_merge(I) obs: 0.12 / R_pim(I) all: 0.034 / R_rim(I) all: 0.125 / Net I/σ(I): 12.3

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	% possible all
2.7-2.79	11.2	1.069	4339	0.84	0.32	1.118	100
2.7-2.797	12.3	0.052	941	0.984	0.016	0.055	99.5

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
PHENIX	1.17.1_3660	refinement
MOSFLM		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4C0S

4c0s

Resolution: 2.7→57.82 Å / SU ML: 0.4198 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 24.302
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2241	4337	5.19 %	RANDOM
R_work	0.1788	79269	-	-
obs	0.1811	83606	99.91 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 78.08 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→57.82 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6936	0	55	117	7108

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0027	7132
X-RAY DIFFRACTION	f_angle_d	0.6347	9698
X-RAY DIFFRACTION	f_chiral_restr	0.0474	1090
X-RAY DIFFRACTION	f_plane_restr	0.0048	1231
X-RAY DIFFRACTION	f_dihedral_angle_d	20.193	2561

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 (%)
2.7-2.73	0.365	152	0.3287	2659	X-RAY DIFFRACTION	99.65
2.73-2.76	0.4016	139	0.3326	2615	X-RAY DIFFRACTION	99.75
2.76-2.8	0.3842	136	0.3193	2671	X-RAY DIFFRACTION	99.72
2.8-2.83	0.3135	155	0.3044	2633	X-RAY DIFFRACTION	100
2.83-2.87	0.345	107	0.2974	2650	X-RAY DIFFRACTION	99.75
2.87-2.91	0.3114	164	0.3015	2634	X-RAY DIFFRACTION	99.86
2.91-2.95	0.3473	150	0.2792	2635	X-RAY DIFFRACTION	99.79
2.95-2.99	0.2674	143	0.2595	2630	X-RAY DIFFRACTION	99.78
2.99-3.04	0.3295	128	0.2635	2675	X-RAY DIFFRACTION	99.96
3.04-3.09	0.2775	174	0.2506	2616	X-RAY DIFFRACTION	99.86
3.09-3.14	0.2935	148	0.252	2609	X-RAY DIFFRACTION	99.96
3.14-3.2	0.3124	153	0.2434	2637	X-RAY DIFFRACTION	99.93
3.2-3.26	0.3062	136	0.2367	2659	X-RAY DIFFRACTION	99.89
3.26-3.33	0.27	145	0.2322	2641	X-RAY DIFFRACTION	99.96
3.33-3.4	0.2855	155	0.2125	2649	X-RAY DIFFRACTION	100
3.4-3.48	0.2455	130	0.1804	2629	X-RAY DIFFRACTION	100
3.48-3.57	0.1794	154	0.1744	2635	X-RAY DIFFRACTION	99.89
3.57-3.66	0.1716	138	0.1555	2641	X-RAY DIFFRACTION	99.96
3.66-3.77	0.1774	146	0.1543	2660	X-RAY DIFFRACTION	99.96
3.77-3.89	0.1856	120	0.1523	2655	X-RAY DIFFRACTION	100
3.89-4.03	0.1798	142	0.143	2661	X-RAY DIFFRACTION	100
4.03-4.19	0.1832	190	0.1263	2597	X-RAY DIFFRACTION	99.96
4.19-4.39	0.1908	166	0.1287	2606	X-RAY DIFFRACTION	100
4.39-4.62	0.1825	142	0.1218	2681	X-RAY DIFFRACTION	100
4.62-4.9	0.1517	138	0.117	2644	X-RAY DIFFRACTION	100
4.91-5.28	0.2046	149	0.1354	2614	X-RAY DIFFRACTION	100
5.28-5.81	0.189	145	0.156	2661	X-RAY DIFFRACTION	100
5.82-6.65	0.2212	144	0.1664	2645	X-RAY DIFFRACTION	100
6.66-8.38	0.2082	131	0.1797	2649	X-RAY DIFFRACTION	100
8.38-57.82	0.226	117	0.1736	2678	X-RAY DIFFRACTION	99.75

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	7.35616850523	-1.18138535738	2.34218169469	2.18916458553	1.00921310221	6.53657293694	-0.0816461168562	-0.0763722048532	-0.0239144181995	-0.36955483085	-0.0205138244316	0.386822805744	0.210288032432	-0.727883106406	0.0583690774138	0.793922233178	-0.193440575078	0.102034357388	0.375013483187	-0.067261826755	0.535358519887	47.2869619341	3.27568941236	-35.898606812
2	4.13866361248	-0.20382706199	1.98218165008	8.9859502716	1.15217301338	4.2571982778	-0.0992629803635	0.132981822322	0.248213481598	-0.0802343089913	0.0608266077664	-0.784849223984	0.313222067456	0.157716089258	0.0328886554497	0.624789488378	-0.0486661108078	0.0680362993307	0.289803046905	0.0273431681894	0.4354112308	63.5206523572	2.66447536173	-33.2314901593
3	4.63438158814	0.675657572412	1.61798371804	4.8691569039	0.471158072263	3.00275893996	-0.137500261089	-0.284310221027	-0.275119479427	0.453388637753	0.143606278511	-0.173083038338	1.1601380916	0.0313578741824	-0.013810279906	1.08654366942	-0.0246354980075	0.0919648622863	0.373211117276	-0.0161417343618	0.472696175731	62.1560306601	-9.47152718781	-28.0120542423
4	3.57931414517	-1.16013757579	-0.843608812117	2.59047684832	4.10988782897	8.18002514954	-0.255663939022	-0.161075010028	-0.128018964178	1.6257829503	0.136499531264	0.503384358446	0.622926746596	-0.811220953236	0.0946735850041	0.744930655127	0.00849379477647	0.0450313953407	0.406482455561	0.0383499016923	0.531329149899	56.1466344137	21.904343652	-0.0889146708292
5	5.91981781608	0.782393775786	-2.77630334115	8.20502099356	0.352751343283	7.04711656645	-0.403563435092	-0.0202252261986	-0.241962393112	1.2012492821	0.458408834776	0.521047127201	0.783012807733	-0.952460024276	-0.0300335922028	0.989706104055	-0.0469752623767	0.0511060875125	0.580432957247	0.0776637979355	0.384505961707	55.5433266445	17.8367574888	5.02819487333
6	9.03163924809	-2.32768668119	-2.82154911203	7.56587748564	-0.259688667864	4.18426616712	0.189584278129	-0.701659583667	-0.172376223671	1.37704454119	0.0276840137615	-0.579609764253	0.472870353178	0.50421778018	-0.127117770004	0.793067347365	0.0341055795599	-0.137126513669	0.451903174393	-0.0153083291616	0.450946788364	63.3929382449	22.7862637535	2.08474886835
7	4.77828325353	0.681286575431	-1.79161387148	4.76573615738	3.10618112601	9.36446826213	-0.194652256655	0.230613892606	-0.109231461902	-0.761812375388	0.280737376061	-0.728764797803	-0.44926154166	0.466729791022	-0.0702292876333	0.581802683315	-0.0105474521278	0.08826643944	0.301105533581	0.0465544338817	0.524718578133	69.7885689562	23.6413504035	-25.7158270652
8	4.98420565683	0.0935643885456	-2.69307364811	4.7279432053	1.4967128295	3.94215884135	0.103442817076	-0.540762637248	-0.167060325625	0.400282697163	-0.0807286760632	-0.556990836739	0.236921668615	0.581173634094	0.00153167868133	0.458407108051	-0.0434332589336	-0.0445271315402	0.366856993998	-0.0208165695007	0.505895926157	68.1435483282	22.0489407226	-16.714110482
9	7.17080194075	1.16044029168	3.0867249398	4.16158856894	0.00516752290965	4.41017707996	-0.125621615565	-0.280980032569	-0.308521238286	0.670282321688	0.210486229809	-0.348221151455	0.194179974865	-0.178295413019	-0.0229638814537	0.547692329996	0.100285471414	0.0848028908986	0.384109149698	-0.00756847826447	0.367122244635	48.5251900785	38.7872486734	-10.5673929678
10	3.50082358318	-1.76333639678	-0.852295759763	9.05164843513	2.84571130116	5.06216696037	-0.189274727244	-0.144741537864	-0.231016173392	-0.130443637762	0.484360039058	-0.408142400727	0.245351712525	0.262225769827	-0.075586411382	0.459484695372	0.109133439728	-0.0161257847664	0.571876292285	-0.0055840579302	0.36026639034	49.1397240944	34.345654869	-14.4303563332
11	2.72724985351	-1.45024695711	-1.42295094168	4.23801776372	2.02106131905	5.80441707046	-0.0575024234564	0.0292028113478	-0.176469149539	0.0598636580373	0.0528955207653	0.610423446176	-0.0297782614183	-0.692024108265	-0.00862601129656	0.287296506903	0.0262184893152	0.0571966879221	0.449985347003	0.0985648569378	0.409018247016	32.0144277348	43.2678613298	-16.9478238462
12	0.0513045812599	0.344784522441	0.51616339694	8.29399616143	8.32595739186	8.67442530664	-0.200368452342	0.0828560677429	-0.65215423981	1.31910576574	-0.0623878296084	0.75887044065	1.32679508505	-0.851306948055	0.244030379115	0.685986680509	-0.0865677510508	0.211445470484	0.681081727979	0.100358007872	0.822921299002	28.2378602027	25.8711668719	-13.2208679171
13	3.69139694474	1.60293473817	-0.680478262106	8.52940433491	-1.05657897927	2.94977017288	-0.131115308319	-0.211236458772	-1.11590102553	-0.478808312157	-0.161290648252	1.91515145374	0.958913767294	-0.89333724565	0.254358391125	0.811092745882	-0.261825352174	0.0669373068794	0.755170593594	-0.0695141839664	1.4158644095	25.0500176042	5.76734356255	-30.5259707771
14	3.21421724241	2.32200854441	0.515341383891	3.14851670866	0.73798377274	7.48077075546	-0.0746712441867	0.661516880076	-0.0925419837583	-1.79803410492	-0.142691353248	0.55977981568	-0.522252870189	-0.429847022803	0.11456162255	0.89690891603	0.0329207021128	-0.122037419408	0.667661116896	-0.00205074371199	0.596800480665	38.1651442821	29.2932719204	-41.941211693
15	4.64652027472	2.03180154732	-0.0503088018704	5.99903682688	-0.281904632061	4.26711703133	-0.0325865509358	0.562589794519	-0.377053716654	-1.18325646354	0.113162076322	1.15379338373	0.312047402426	-0.735832106215	0.0685486927973	0.73105214578	-0.0753972517433	-0.24887709274	0.553834569599	-0.11779889437	0.804227496619	29.1508977126	19.9639737575	-37.931050665

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 92 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 93 through 163 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 164 through 240 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 241 through 269 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 270 through 306 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 307 through 336 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 337 through 389 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 390 through 454 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 4 through 48 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 49 through 92 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 93 through 222 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 223 through 249 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 250 through 346 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 347 through 389 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 390 through 461 )

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Elongation factor 1-alpha ... , 2 types, 2 molecules AB

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Non-polymers , 5 types, 139 molecules

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Details

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-Elongation factor 1-alpha ... , 2 types, 2 molecules AB

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Elongation factor 1-alpha ... , 2 types, 2 molecules AB

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Non-polymers , 5 types, 139 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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

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Yorodumi