PDB-6vs4: Crystal structure of ADP RIBOSYLATION FACTOR-LIKE GTP BINDING PRO...

ID or keywords:

Entry

Database: PDB / ID: 6vs4

Title

Crystal structure of ADP RIBOSYLATION FACTOR-LIKE GTP BINDING PROTEIN /Small COPII coat GTPase SAR1 from Encephalitozoon cuniculi in complex with GDP

Components

Small COPII coat GTPase SAR1

Keywords

HYDROLASE / SSGCID / COPII coat GTPase SAR1 / ADP RIBOSYLATION FACTOR-LIKE GTP BINDING PROTEIN /

Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

vesicle-mediated transport /

Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement /

intracellular protein transport / ER to Golgi transport vesicle membrane /

Golgi membrane /

GTPase activity / GTP binding / endoplasmic reticulum membrane
Similarity search - Function

Biological species

Encephalitozoon cuniculi (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal structure of ADP RIBOSYLATION FACTOR-LIKE GTP BINDING PROTEIN /Small COPII coat GTPase SAR1 from Encephalitozoon cuniculi in complex with GDP
Authors: Abendroth, J. / Fox III, D. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Feb 10, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 11, 2020	Provider: repository / Type: Initial release
Revision 1.1	Mar 6, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.2	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6vs4.cif.gz	232.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6vs4.ent.gz	156.2 KB	Display	PDB format
PDBx/mmJSON format	6vs4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vs/6vs4 ftp://data.pdbj.org/pub/pdb/validation_reports/vs/6vs4	HTTPS FTP

-
Related structure data

Similar structure data	1p0n-3 1p0k-3 5ijv-2 1j4g-d 1r4a-d 5ahn-1 1vcf-3 1p0k-2 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
Other databases	TargetTrack: EncuA.00324.a

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Small COPII coat GTPase SAR1

B: Small COPII coat GTPase SAR1

hetero molecules

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

1

A: Small COPII coat GTPase SAR1

B: Small COPII coat GTPase SAR1

hetero molecules

A: Small COPII coat GTPase SAR1

B: Small COPII coat GTPase SAR1

hetero molecules

defined by author&software
Evidence: gel filtration
104 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	65.190, 65.190, 307.710
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2
Space group name Hall	P4nw2abw
Symmetry operation	#1: x,y,z #2: -y+1/2,x+1/2,z+3/4 #3: y+1/2,-x+1/2,z+1/4 #4: x+1/2,-y+1/2,-z+1/4 #5: -x+1/2,y+1/2,-z+3/4 #6: -x,-y,z+1/2 #7: y,x,-z #8: -y,-x,-z+1/2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details	Auth asym-ID	Auth seq-ID
1	1	1	(chain 'A' and (resid -1 through 6 or (resid 7...	A	-1 - 164
1	2	1	(chain 'A' and (resid -1 through 6 or (resid 7...	A	166 - 218
1	3	1	(chain 'A' and (resid -1 through 6 or (resid 7...	A	400
2	1	1	(chain 'B' and (resid -1 through 88 or (resid 89...	B	-1 - 164
2	2	1	(chain 'B' and (resid -1 through 88 or (resid 89...	B	166 - 218
2	3	1	(chain 'B' and (resid -1 through 88 or (resid 89...	B	401

#1: Protein	Small COPII coat GTPase SAR1 Mass: 25429.764 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Encephalitozoon cuniculi (strain GB-M1) (fungus) Strain: GB-M1 / Gene: SAR1, ECU05_0090 / Plasmid: EncuA.00324.a.MB1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q8SS09, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#2: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#3: 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 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.24 Å³/Da / Density % sol: 62 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: RigakuReagents JCSG+ screen, condition B10 + 10% RigakuReagents ADDIT G7: 50% (V/V) PEG 200, 200mM MgCl2, 100mM Na-cacodylate pH 6.5 + 10mM spermine: EncuA.00324.a.MB1.PW30297 at 12mg/ml + ...Details: RigakuReagents JCSG+ screen, condition B10 + 10% RigakuReagents ADDIT G7: 50% (V/V) PEG 200, 200mM MgCl2, 100mM Na-cacodylate pH 6.5 + 10mM spermine: EncuA.00324.a.MB1.PW30297 at 12mg/ml + 5mM GDP: cryo: 20% EG: tray: 225442g7: puck txl1-11.

Crystal

Density Matthews: 3.24 Å³/Da / Density % sol: 62 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: RigakuReagents JCSG+ screen, condition B10 + 10% RigakuReagents ADDIT G7: 50% (V/V) PEG 200, 200mM MgCl2, 100mM Na-cacodylate pH 6.5 + 10mM spermine: EncuA.00324.a.MB1.PW30297 at 12mg/ml + ...

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

CLSI

/ Beamline: 08ID-1 / Wavelength: 0.9795 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 20, 2011

Radiation

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

Radiation wavelength

Wavelength: 0.9795 Å / Relative weight: 1

Reflection

Resolution: 2.4→50 Å / Num. obs: 27225 / % possible obs: 99.7 % / Redundancy: 7.025 % / B_iso Wilson estimate: 60.444 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.053 / R_rim(I) all: 0.057 / Χ²: 1.042 / Net I/σ(I): 21.49

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.4-2.46	7.352	0.558	3.29	1952	0.933	0.6	99.9
2.46-2.53	7.276	0.481	3.93	1915	0.931	0.518	100
2.53-2.6	7.252	0.409	4.58	1883	0.953	0.44	100
2.6-2.68	7.354	0.327	5.81	1783	0.966	0.352	100
2.68-2.77	7.272	0.271	6.95	1751	0.976	0.293	99.9
2.77-2.87	7.243	0.197	9.24	1725	0.985	0.212	99.9
2.87-2.98	7.226	0.156	11.67	1670	0.99	0.168	99.9
2.98-3.1	7.212	0.113	15.64	1590	0.996	0.122	99.8
3.1-3.24	7.228	0.089	19.25	1507	0.997	0.095	99.9
3.24-3.39	7.054	0.065	24.17	1476	0.998	0.07	99.8
3.39-3.58	7.039	0.05	30.37	1404	0.999	0.053	99.9
3.58-3.79	6.951	0.04	36.21	1333	0.999	0.043	99.9
3.79-4.06	6.71	0.039	38.86	1268	0.999	0.042	100
4.06-4.38	6.71	0.034	43.21	1184	0.999	0.037	99.9
4.38-4.8	6.657	0.032	46.43	1095	0.999	0.034	99.7
4.8-5.37	6.605	0.029	46.97	1009	0.999	0.031	99.9
5.37-6.2	6.546	0.03	43.85	894	0.999	0.032	99.6
6.2-7.59	6.317	0.026	45.28	779	1	0.029	99.1
7.59-10.73	6.094	0.022	51.88	626	1	0.024	98.6
10.73-50	5.231	0.024	48.63	381	0.999	0.027	92

-
Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	1.17.1	refinement
PDB_EXTRACT	3.25	data extraction
MR-Rosetta		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: MR rosetta based on top 16 HHPRED results

Resolution: 2.4→45.59 Å / SU ML: 0.3005 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.6956

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.235	1933	7.13 %	0
R_work	0.1804	-	-	-
obs	0.1843	27104	99.7 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 66.57 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→45.59 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3511	0	21	87	3619

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0042	3613
X-RAY DIFFRACTION	f_angle_d	0.6768	4923
X-RAY DIFFRACTION	f_chiral_restr	0.0481	561
X-RAY DIFFRACTION	f_plane_restr	0.0043	646
X-RAY DIFFRACTION	f_dihedral_angle_d	18.3235	1297

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 (%)
2.4-2.46	0.3276	131	0.2578	1725	X-RAY DIFFRACTION	99.52
2.46-2.53	0.2953	134	0.2301	1772	X-RAY DIFFRACTION	99.95
2.53-2.6	0.2956	122	0.2365	1788	X-RAY DIFFRACTION	99.84
2.6-2.68	0.2909	125	0.2335	1746	X-RAY DIFFRACTION	99.84
2.69-2.78	0.2739	143	0.2225	1758	X-RAY DIFFRACTION	99.89
2.78-2.89	0.3053	144	0.2146	1762	X-RAY DIFFRACTION	99.9
2.89-3.02	0.2671	139	0.2151	1763	X-RAY DIFFRACTION	99.74
3.02-3.18	0.3047	143	0.2107	1780	X-RAY DIFFRACTION	99.69
3.18-3.38	0.2654	132	0.202	1795	X-RAY DIFFRACTION	99.9
3.38-3.64	0.2275	135	0.1815	1804	X-RAY DIFFRACTION	99.79
3.64-4.01	0.2093	150	0.1669	1794	X-RAY DIFFRACTION	100
4.01-4.59	0.1701	134	0.1435	1848	X-RAY DIFFRACTION	99.9
4.59-5.78	0.1942	143	0.1495	1861	X-RAY DIFFRACTION	99.7
5.78-45.59	0.242	158	0.1736	1975	X-RAY DIFFRACTION	98.29

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	4.51328963576	-6.4568872206	5.06008663379	5.32174959172	-4.79583573208	4.99868972616	0.31221755194	0.17310849115	-0.360533351202	-0.606959555103	-0.273316028778	0.328809813518	0.424784067111	-0.304010526888	-0.0584910213312	0.363991271094	0.0750992026707	0.000864957652912	0.427532159269	-0.0119952486264	0.439092742882	27.7750590242	28.3550834737	148.801565669
2	8.93330794845	0.746596893689	-0.355260418297	4.18939936005	-1.45507908446	0.758723307792	-0.4136983031	0.308287268667	-0.500572879185	0.253666578994	0.417020563229	-0.0315817358845	0.616905174397	-1.0912097171	0.0572342875644	0.420623500591	-0.049789557772	0.0773281528433	0.701859299215	0.0354029467819	0.505629695072	8.50043508301	36.5352097118	133.357713387
3	3.32052230524	-0.587955527135	3.19632703724	2.73115157169	-1.3856379965	3.83637355514	-0.055765840608	1.06944576302	0.211966077996	-0.0646891672803	0.199732713733	0.460984876685	-0.193746851764	-1.63591411906	-0.132816269926	0.425778997687	-0.0532153582677	0.0569665655118	1.04774118126	0.0248281874866	0.550395325307	6.13329839543	41.1183663253	125.764329944
4	6.43830304061	-0.75987734704	-2.16445318056	3.09621562914	-0.327505725912	6.01044652242	-0.00199714351055	1.09202840513	0.634775439307	-0.130120093683	0.0850948255449	-0.0656953385746	-0.359766858814	-0.287073608276	-0.0375479435025	0.3569081797	0.010644911897	0.0258656875362	0.587619490107	0.170649860924	0.53094773903	19.2415326337	47.8136042584	125.35485561
5	7.59609375992	-6.17629248474	-3.35995412377	9.37810045363	4.68215650921	5.54616782205	0.281268368013	0.250337019185	0.372104093067	-0.579186672972	-0.123048416732	-0.545591151769	-0.185108010642	0.380140142882	-0.108170531313	0.365739062426	0.00568685853411	0.0477046261932	0.396701403222	0.0432688178995	0.304902982399	37.3582013831	30.9799158269	148.299159576
6	7.52331888609	0.544607217889	1.0735617637	4.85780488327	0.569360078115	6.26247574579	-0.190051194622	-0.0472833564518	0.516557861003	0.0624320247868	0.223395852226	-0.534575137048	-0.67648918625	0.760684422519	0.024324051376	0.372837768093	0.0658857355655	0.0531392913342	0.565273291859	-0.0152731978417	0.493151844583	56.1885776246	19.6330617025	134.980688934
7	5.15420603763	-1.33364708555	-4.3607965254	3.2909089995	1.07363419882	4.76277965238	-0.13506479117	0.203276330969	-0.317183741318	0.0248703347187	-0.0159543464522	-0.408269125415	0.261494230177	0.191553464379	0.0492772801808	0.282265780111	0.0147799477067	0.0494825857486	0.656028202758	-0.0576311466256	0.535762260231	60.9153293518	14.6428601625	129.050723599
8	5.15355118263	-0.189500779787	-0.693890244854	3.09137760981	0.358009877839	6.56690014088	-0.249014132098	0.575035980745	-0.823176175586	-0.0938273206447	0.0588780735011	-0.0722760615426	0.490176548489	-0.213752523985	0.148992943963	0.367922646017	0.00164878237714	0.066313989159	0.423594130768	-0.0868033156706	0.513293060166	47.5441198531	7.05887425854	130.032153162

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 29 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 30 through 70 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 71 through 114 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 115 through 221 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid -3 through 31 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 32 through 70 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 71 through 96 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 97 through 219 )

-
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