PDB-2bjn: X-ray Structure of human TPC6

ID or keywords:

Entry

Database: PDB / ID: 2bjn

Title

X-ray Structure of human TPC6

Components

TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 6B

Keywords

TRANSPORT PROTEIN / TPC6 /

TRAPP COMPLEX /

TETHERING

Function / homology

Function and homology information

vesicle coating / vesicle tethering / TRAPPII protein complex /

TRAPP complex / cis-Golgi network / RAB GEFs exchange GTP for GDP on RABs / COPII-mediated vesicle transport / endoplasmic reticulum to Golgi vesicle-mediated transport /

regulation of GTPase activity /

trans-Golgi network ...
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.7 Å

Authors

Kummel, D. / Mueller, J.J. / Roske, Y. / Misselwitz, R. / Bussow, K. / Heinemann, U.

Citation

Journal: Embo Rep. / Year: 2005
Title: The Structure of the Trapp Subunit Tpc6 Suggests a Model for a Trapp Subcomplex.
Authors: Kummel, D. / Mueller, J.J. / Roske, Y. / Misselwitz, R. / Bussow, K. / Heinemann, U.

History

Deposition	Feb 4, 2005	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 20, 2005	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance

Remark 650

HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2bjn.cif.gz	71.7 KB	Display	PDBx/mmCIF format
PDB format	pdb2bjn.ent.gz	59.7 KB	Display	PDB format
PDBx/mmJSON format	2bjn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2bjn_validation.pdf.gz	298.4 KB	Display	wwPDB validaton report
Full document	2bjn_full_validation.pdf.gz	302.5 KB	Display
Data in XML	2bjn_validation.xml.gz	9.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bj/2bjn ftp://data.pdbj.org/pub/pdb/validation_reports/bj/2bjn	HTTPS FTP

-
Related structure data

Similar structure data	7o94-2 2hak-8 4d4r-1 6hd6-1 2c27-d 3doa-d 6euv-4 4r8m-2 6fnh-3 6lz2-1 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
Related items in Molecule of the Month	#133 - Jan 2011 Nitric Oxide Synthase similarity (1) #53 - May 2004 Serpins similarity (1) #205 - Jan 2017 Nuclear Pore Complex similarity (1)

Deposited unit

A: TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 6B

B: TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 6B

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	99.423, 57.005, 60.406
Angle α, β, γ (deg.)	90.00, 117.16, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 6B / TPC6 Mass: 18151.119 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Description: RZPD, GERMAN RESOURCE CENTRE / Plasmid: PQTEV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SCS1 ROSETTA / References: UniProt: Q86SZ2
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.1 Å³/Da / Density % sol: 41 %
Crystal grow	pH: 7.5 Details: 22-23%PEG3350,0.1M HEPES PH7.5, 0.3M(NH4)2SO4, pH 7.50

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184
Detector	Type: MARRESEARCH / Detector: CCD / Date: Aug 6, 2004 / Details: MIRRORS
Radiation	Monochromator: SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.7→23 Å / Num. obs: 32829 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / R_sym value: 0.05 / Net I/σ(I): 22.81
Reflection shell	Resolution: 1.7→1.76 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.27 / R_sym value: 0.48 / % possible all: 89.9

-
Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
HKL-2000		data reduction
HKL-2000		data scaling
SOLVE/RESOLVE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.7→22.98 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.947 / SU B: 3.902 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.209	1697	5.2 %	RANDOM
R_work	0.175	-	-	-
obs	0.177	31019	98.6 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 31.48 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.51 Å²	0 Å²	-1.35 Å²
2-	-	0.91 Å²	0 Å²
3-	-	-	-1.63 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→22.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2297	0	49	126	2472

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.022	2401
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	2240
X-RAY DIFFRACTION	r_angle_refined_deg	1.741	1.975	3207
X-RAY DIFFRACTION	r_angle_other_deg	1.525	3	5213
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.405	5	285
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.723	24.167	108
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.258	15	470
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.207	15	15
X-RAY DIFFRACTION	r_chiral_restr	0.1	0.2	357
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	2557
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	484
X-RAY DIFFRACTION	r_nbd_refined	0.268	0.3	524
X-RAY DIFFRACTION	r_nbd_other	0.209	0.3	2275
X-RAY DIFFRACTION	r_nbtor_refined	0.192	0.5	1167
X-RAY DIFFRACTION	r_nbtor_other	0.094	0.5	1370
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.225	0.5	249
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	0.293	0.3	26
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.357	0.3	48
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.219	0.5	29
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	1.125	1.5	1468
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.449	2	2298
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.274	3	1028
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.22	4.5	909
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

LS refinement shell

Resolution: 1.7→1.74 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.324	90
R_work	0.241	2072

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	26.5561	-5.0414	0.9193	2.8033	-0.2359	1.5575	0.0447	0.1856	0.0051	-0.0997	-0.0016	0.0824	0.0786	0.1573	-0.043	-0.1608	0.0202	0.0206	-0.1563	0.0276	-0.1815	19.3264	-4.7995	22.6044
2	9.1193	-1.8592	2.7469	24.2155	-5.9614	2.939	0.0353	-0.5744	-1.0266	0.2011	0.3696	2.3021	0.4106	-1.1576	-0.4049	-0.0596	-0.0527	0.002	0.0254	0.0381	0.2269	-1.4868	-0.033	20.7058
3	18.5846	4.4472	3.207	6.1421	0.7442	4.0472	-0.102	-0.0706	0.1529	0.0576	-0.17	-0.1333	-0.0965	0.3408	0.2721	-0.1652	0.0306	-0.0232	-0.2122	0.0495	-0.1773	14.9473	9.5912	19.9343
4	1.4921	0.4693	0.2248	14.7611	-6.13	10.4191	0.0382	0.8944	0.441	-0.3646	-0.375	-0.6498	-0.4199	1.4209	0.3368	-0.0992	-0.0493	0.0515	0.3679	0.1983	0.0243	26.4335	9.5244	10.2818
5	4.789	-4.7923	4.2109	11.6221	-6.491	11.4704	0.3179	1.1618	0.2514	-1.0454	-0.5954	-0.2639	0.0961	1.115	0.2775	0.029	0.0533	0.0869	0.4737	0.1364	-0.0045	23.26	7.0879	2.0783
6	6.5216	-0.9664	-0.8468	12.1799	-5.2417	8.8341	-0.0028	0.8971	-0.5769	-0.7239	-0.2238	-0.2811	0.8787	0.6731	0.2266	-0.0041	0.1394	0.0387	0.1955	-0.0278	-0.0754	20.9677	-2.9129	8.9685
7	3.8229	2.042	-0.5959	14.558	0.2433	3.0901	-0.0786	0.4127	-0.0361	-0.5353	0.0365	0.1114	0.0803	0.1801	0.0421	-0.1667	0.029	-0.0275	-0.0965	0.0456	-0.1801	14.848	6.6553	13.6607
8	6.1295	2.7406	1.2627	6.7127	1.8391	4.4638	-0.1404	0.6742	-0.4014	-1.6163	0.1746	0.3819	0.0197	0.254	-0.0342	-0.0157	0.0395	0.0058	0.0732	0.0389	-0.1198	14.729	4.8312	6.4165
9	7.4438	-9.4964	1.8266	26.8399	0.3269	6.0325	0.2133	0.894	0.1931	-0.998	-0.5525	-0.1489	-0.1097	0.4852	0.3391	0.0158	0.0414	0.0053	0.2032	0.1389	-0.1148	15.6852	8.7302	4.0684
10	17.7471	-0.0228	-6.6255	5.5048	-1.4564	9.2833	0.1161	0.0917	0.2586	-0.0973	-0.354	-0.4005	-0.3171	0.6882	0.2379	-0.1011	0.0221	-0.039	-0.1102	0.0882	-0.1036	20.4822	5.9295	27.7738
11	5.4031	-0.7506	-0.5679	22.6546	-12.525	14.6951	0.2247	-0.1599	0.4726	0.5461	0.6289	2.4915	-0.6517	-2.0182	-0.8536	-0.0038	0.13	0.0857	0.1389	-0.0178	0.2454	1.7062	1.5717	36.6248
12	10.0117	-4.4971	-5.5427	8.8214	3.0449	6.2581	0.2082	-0.0621	0.1699	0.0086	-0.1243	0.3452	-0.1332	-0.1664	-0.0839	-0.2007	-0.0063	-0.015	-0.2287	0.0029	-0.1883	15.0783	-7.4083	33.1756
13	0.0805	0.3282	0.1455	1.6003	2.5669	15.1028	0.1606	-0.0832	-0.6336	-0.0367	0.031	-0.4346	1.7668	1.0233	-0.1916	0.0565	0.0981	0.0073	0.0963	0.0639	0.055	32.4817	-17.0653	33.7634
14	3.1693	-2.6148	3.1578	8.8814	-4.0505	7.8934	0.0712	0.0391	-0.0482	0.1617	-0.0186	-0.1987	0.0522	0.2334	-0.0525	-0.1972	-0.0056	-0.0008	-0.1423	-0.0019	-0.1808	30.2917	-6.9909	35.9604
15	4.0188	2.2861	-0.7403	10.4135	-9.7622	15.7444	0.154	-0.4136	0.0382	0.4962	-0.4245	-0.3217	-0.0909	0.7116	0.2705	-0.0506	0.0168	-0.0557	-0.1215	0.001	-0.1351	31.1589	-5.9709	45.6695
16	6.2461	-1.2783	4.0217	11.5341	-8.1701	14.4803	-0.2817	0.1127	0.679	0.6627	-0.1137	-0.2474	-1.1484	0.3066	0.3954	0.0191	-0.037	-0.0322	-0.1563	-0.0311	-0.1121	26.6572	4.1587	40.5298
17	3.9111	-1.9994	0.9785	11.7373	-1.1222	3.2851	-0.0434	-0.2226	0.0932	0.549	-0.0074	0.4604	-0.3336	-0.1889	0.0507	-0.1636	-0.0051	0.0012	-0.1785	-0.0093	-0.2066	18.6439	-4.4039	38.2049
18	3.4183	1.827	0.3938	15.657	3.8115	4.0254	0.2486	-0.3852	0.3448	0.8556	-0.4193	0.2883	-0.2258	-0.2228	0.1707	-0.0346	-0.0012	-0.0084	-0.1073	-0.0091	-0.1648	22.0378	-2.6757	45.128
19	8.0461	9.8719	2.6919	45.3473	3.758	6.1204	0.3848	-0.6929	-0.3096	0.615	-0.3419	0.3159	0.7872	-0.8041	-0.0429	0.1073	-0.0506	-0.0801	-0.1138	0.0457	-0.1709	21.9587	-12.0574	47.434

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 20
2	X-RAY DIFFRACTION	2	A	21 - 33
3	X-RAY DIFFRACTION	3	A	34 - 53
4	X-RAY DIFFRACTION	4	A	63 - 79
5	X-RAY DIFFRACTION	5	A	80 - 94
6	X-RAY DIFFRACTION	6	A	95 - 105
7	X-RAY DIFFRACTION	7	A	117 - 135
8	X-RAY DIFFRACTION	8	A	136 - 150
9	X-RAY DIFFRACTION	9	A	151 - 158
10	X-RAY DIFFRACTION	10	B	1 - 20
11	X-RAY DIFFRACTION	11	B	21 - 34
12	X-RAY DIFFRACTION	12	B	35 - 50
13	X-RAY DIFFRACTION	13	B	51 - 65
14	X-RAY DIFFRACTION	14	B	66 - 79
15	X-RAY DIFFRACTION	15	B	80 - 94
16	X-RAY DIFFRACTION	16	B	95 - 105
17	X-RAY DIFFRACTION	17	B	116 - 135
18	X-RAY DIFFRACTION	18	B	136 - 153
19	X-RAY DIFFRACTION	19	B	154 - 158

-
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