[English] 日本語
Yorodumi
- PDB-6z1n: Structure of the human heterotetrameric cis-prenyltransferase complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6z1n
TitleStructure of the human heterotetrameric cis-prenyltransferase complex
Components(Dehydrodolichyl diphosphate synthase complex subunit ...) x 2
KeywordsTRANSFERASE / dolichol / cis-prenyltransferase / NgBR / DHDDS / Nogo-B receptor
Function / homology
Function and homology information


dolichyl diphosphate biosynthetic process / protein mannosylation / Defective DHDDS causes RP59 / dolichol biosynthetic process / dehydrodolichyl diphosphate synthase complex / Synthesis of Dolichyl-phosphate / regulation of intracellular cholesterol transport / ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] / dehydrodolichyl diphosphate synthase activity / polyprenol biosynthetic process ...dolichyl diphosphate biosynthetic process / protein mannosylation / Defective DHDDS causes RP59 / dolichol biosynthetic process / dehydrodolichyl diphosphate synthase complex / Synthesis of Dolichyl-phosphate / regulation of intracellular cholesterol transport / ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] / dehydrodolichyl diphosphate synthase activity / polyprenol biosynthetic process / vascular endothelial growth factor signaling pathway / protein glycosylation / positive regulation of blood vessel endothelial cell migration / cholesterol homeostasis / positive regulation of nitric-oxide synthase activity / angiogenesis / cell differentiation / endoplasmic reticulum membrane / endoplasmic reticulum / metal ion binding
Similarity search - Function
Dehydrodolichyl diphosphate synthase complex subunit Nus1 / Di-trans-poly-cis-decaprenylcistransferase-like, conserved site / Undecaprenyl pyrophosphate synthase family signature. / Decaprenyl diphosphate synthase-like / Putative undecaprenyl diphosphate synthase / Decaprenyl diphosphate synthase-like superfamily
Similarity search - Domain/homology
FARNESYL DIPHOSPHATE / PHOSPHATE ION / Dehydrodolichyl diphosphate synthase complex subunit DHDDS / Dehydrodolichyl diphosphate synthase complex subunit NUS1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLisnyansky Bar-El, M. / Haitin, Y. / Giladi, M.
Funding support Israel, 5items
OrganizationGrant numberCountry
Israel Science Foundation1721/16 Israel
Israel Science Foundation1775/12 Israel
Other privateICRF-01214 Israel
Other privateICRF-19202 Israel
German-Israeli Foundation for Research and DevelopmentI2425418.13-2016 Israel
CitationJournal: Nat Commun / Year: 2020
Title: Structural basis of heterotetrameric assembly and disease mutations in the human cis-prenyltransferase complex.
Authors: Bar-El, M.L. / Vankova, P. / Yeheskel, A. / Simhaev, L. / Engel, H. / Man, P. / Haitin, Y. / Giladi, M.
History
DepositionMay 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2024Group: 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 visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dehydrodolichyl diphosphate synthase complex subunit DHDDS
B: Dehydrodolichyl diphosphate synthase complex subunit NUS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9155
Polymers63,4142
Non-polymers5023
Water2,198122
1
A: Dehydrodolichyl diphosphate synthase complex subunit DHDDS
B: Dehydrodolichyl diphosphate synthase complex subunit NUS1
hetero molecules

A: Dehydrodolichyl diphosphate synthase complex subunit DHDDS
B: Dehydrodolichyl diphosphate synthase complex subunit NUS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,83010
Polymers126,8274
Non-polymers1,0036
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_566x-y+2/3,-y+4/3,-z+4/31
Buried area12430 Å2
ΔGint-95 kcal/mol
Surface area45160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.074, 184.074, 112.593
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-557-

HOH

-
Components

-
Dehydrodolichyl diphosphate synthase complex subunit ... , 2 types, 2 molecules AB

#1: Protein Dehydrodolichyl diphosphate synthase complex subunit DHDDS / Cis-isoprenyltransferase / Cis-IPTase / Cis-prenyltransferase subunit hCIT / Epididymis tissue protein Li 189m


Mass: 39201.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHDDS, HDS / Production host: Escherichia coli (E. coli)
References: UniProt: Q86SQ9, ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific]
#2: Protein Dehydrodolichyl diphosphate synthase complex subunit NUS1 / Cis-prenyltransferase subunit NgBR / Nogo-B receptor / NgBR / Nuclear undecaprenyl pyrophosphate ...Cis-prenyltransferase subunit NgBR / Nogo-B receptor / NgBR / Nuclear undecaprenyl pyrophosphate synthase 1 homolog


Mass: 24211.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUS1, C6orf68, NGBR / Production host: Escherichia coli (E. coli)
References: UniProt: Q96E22, ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific]

-
Non-polymers , 4 types, 125 molecules

#3: Chemical ChemComp-FPP / FARNESYL DIPHOSPHATE


Mass: 382.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.8 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.1 M NaCl, 0.1 M NaP pH 7.0, 33% w/v PEG 300, 760 mM FPP

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.3→46.019 Å / Num. obs: 32476 / % possible obs: 100 % / Redundancy: 21.1 % / CC1/2: 0.999 / Rrim(I) all: 0.17 / Net I/σ(I): 16.32
Reflection shellResolution: 2.3→2.44 Å / Mean I/σ(I) obs: 1.56 / Num. unique obs: 5182 / CC1/2: 0.677 / Rrim(I) all: 1.978 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1x09

1x09


Resolution: 2.3→45.983 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 24.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2229 1633 5.03 %
Rwork0.1888 --
obs0.1905 32473 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→45.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4061 0 30 122 4213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054193
X-RAY DIFFRACTIONf_angle_d0.7015693
X-RAY DIFFRACTIONf_dihedral_angle_d6.8723416
X-RAY DIFFRACTIONf_chiral_restr0.041635
X-RAY DIFFRACTIONf_plane_restr0.004738
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3004-2.36810.36561370.29192536X-RAY DIFFRACTION100
2.3681-2.44460.31991300.2552561X-RAY DIFFRACTION100
2.4446-2.53190.30451340.23632546X-RAY DIFFRACTION100
2.5319-2.63330.27271370.21822562X-RAY DIFFRACTION100
2.6333-2.75310.2751360.21812540X-RAY DIFFRACTION100
2.7531-2.89830.26771330.22182565X-RAY DIFFRACTION100
2.8983-3.07980.30151390.22372543X-RAY DIFFRACTION100
3.0798-3.31750.26931370.21052587X-RAY DIFFRACTION100
3.3175-3.65130.20911320.19152563X-RAY DIFFRACTION100
3.6513-4.17930.17511370.15692588X-RAY DIFFRACTION100
4.1793-5.26430.18151390.1482592X-RAY DIFFRACTION100
5.2643-45.9830.18631420.17982657X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL11 (°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)
12.96942.8026-1.58768.1889-3.22864.91020.13620.2920.7044-0.2626-0.01370.2691-0.16940.2581-0.16380.33580.06360.04810.5237-0.00210.53755.8531119.933836.4353
24.1440.0406-1.81791.01010.40142.99010.23570.25420.5267-0.04360.058-0.1699-0.3773-0.1335-0.29390.36890.01160.03980.320.04850.397625.6529125.677132.1587
31.296-0.07780.64070.7022-0.22012.1865-0.0753-0.08450.14770.13470.0522-0.0563-0.0875-0.00150.01780.35230.0139-0.02850.3935-0.05840.41430.6267113.789748.7707
41.86530.0288-0.10244.8031-5.72598.5414-0.3458-0.09730.15310.26770.3076-0.0445-0.2385-0.69070.16810.6565-0.0555-0.10870.448-0.11290.507439.8387123.809467.5903
58.4666-4.69822.70038.2723-4.21932.242-0.2067-0.0521-0.1816-0.49840.015-0.46551.65760.08840.52920.87230.0315-0.00650.525-0.0520.510643.572979.4930.1059
62.0298-0.6415-0.02372.24540.47383.12150.0049-0.24410.01540.21580.0951-0.11020.17940.0245-0.01280.3550.047-0.07480.3443-0.03220.318236.407291.623345.0442
78.6228-4.2792-0.32365.85093.45894.1747-0.8275-0.8075-0.1840.6380.47370.46991.10571.00020.04420.65550.0952-0.09820.58120.11690.415842.236181.990450.3242
81.6067-1.64980.08373.0318-0.47630.1063-0.0161-0.04160.37930.0259-0.1061-0.44110.03430.20250.09630.47820.055-0.06090.6181-0.03040.463347.2904102.486951.8942
91.51870.60990.52383.66830.78062.0041-0.04650.01710.01920.04480.1728-0.5044-0.03370.2904-0.1610.3360.0108-0.04780.4693-0.06230.434339.8026105.271843.5437
101.15521.8835-1.16057.1983-2.14441.1771-0.2051-0.03320.2808-0.73960.1620.64470.2896-0.3648-0.00730.51460.0328-0.09590.472-0.07660.387434.599396.04829.1055
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 157 )
3X-RAY DIFFRACTION3chain 'A' and (resid 158 through 282 )
4X-RAY DIFFRACTION4chain 'A' and (resid 283 through 326 )
5X-RAY DIFFRACTION5chain 'B' and (resid 79 through 93 )
6X-RAY DIFFRACTION6chain 'B' and (resid 94 through 144 )
7X-RAY DIFFRACTION7chain 'B' and (resid 145 through 176 )
8X-RAY DIFFRACTION8chain 'B' and (resid 177 through 212 )
9X-RAY DIFFRACTION9chain 'B' and (resid 213 through 273 )
10X-RAY DIFFRACTION10chain 'B' and (resid 274 through 293 )

+
About Yorodumi

-
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

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

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

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more