[English] 日本語
Yorodumi
- PDB-7pb1: Structure of the human heterotetrameric cis-prenyltransferase com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pb1
TitleStructure of the human heterotetrameric cis-prenyltransferase complex in complex with magnesium, GGPP and IsPP
Components(Dehydrodolichyl diphosphate synthase complex subunit ...) x 2
KeywordsTRANSFERASE / DHDDS / NgBR / hcit / cis-prenyltransferase / dolichol
Function / homology
Function and homology information


protein mannosylation / Defective DHDDS causes RP59 / dolichol biosynthetic process / dehydrodolichyl diphosphate synthase complex / Synthesis of Dolichyl-phosphate / dolichyl diphosphate biosynthetic process / regulation of intracellular cholesterol transport / ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] / dehydrodolichyl diphosphate synthase activity / polyprenol biosynthetic process ...protein mannosylation / Defective DHDDS causes RP59 / dolichol biosynthetic process / dehydrodolichyl diphosphate synthase complex / Synthesis of Dolichyl-phosphate / dolichyl diphosphate biosynthetic process / regulation of intracellular cholesterol transport / ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] / dehydrodolichyl diphosphate synthase activity / polyprenol biosynthetic process / polyprenyltransferase activity / vascular endothelial growth factor signaling pathway / protein glycosylation / positive regulation of blood vessel endothelial cell migration / lipid droplet / 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
GERANYLGERANYL DIPHOSPHATE / Chem-ISY / 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: 2.59 Å
AuthorsGiladi, M. / Lisnyansky Bar-El, M. / Haitin, Y.
Funding support Israel, 7items
OrganizationGrant numberCountry
Other privateICRF-19202 Israel
Israel Science Foundation1721/16 Israel
Other privateRecanati Foundation for Medical Research Israel
German-Israeli Foundation for Research and DevelopmentI2425418.13/2016 Israel
Other governmentICORE-1775/12 Israel
Other privateTel Aviv Sourasky Medical Center Orion Project Israel
Other privateICA-20200037 Israel
CitationJournal: Sci Adv / Year: 2022
Title: Structural basis for long-chain isoprenoid synthesis by cis -prenyltransferases.
Authors: Giladi, M. / Lisnyansky Bar-El, M. / Vankova, P. / Ferofontov, A. / Melvin, E. / Alkaderi, S. / Kavan, D. / Redko, B. / Haimov, E. / Wiener, R. / Man, P. / Haitin, Y.
History
DepositionJul 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
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)64,1505
Polymers63,4142
Non-polymers7373
Water362
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)128,30110
Polymers126,8274
Non-polymers1,4746
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Unit cell
Length a, b, c (Å)183.470, 183.470, 112.290
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
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, 5 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GRG / GERANYLGERANYL DIPHOSPHATE / Geranylgeranyl pyrophosphate


Mass: 450.443 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C20H36O7P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ISY / 3-methylbut-3-enylsulfanyl(phosphonooxy)phosphinic acid / Isopentyl S-Thiolodiphosphate


Mass: 262.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O6P2S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.89 Å3/Da / Density % sol: 57.4 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.07 M MES, 25% w/v PEG 400, 1.5 mM MgCl2, 4.5% v/v ethanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.57→45.867 Å / Num. obs: 20716 / % possible obs: 89.7 % / Redundancy: 6 % / CC1/2: 0.995 / Rrim(I) all: 0.2 / Net I/σ(I): 8.61
Reflection shellResolution: 2.57→2.64 Å / Num. unique obs: 989 / CC1/2: 0.139 / Rrim(I) all: 2.598

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Z1N

6z1n


Resolution: 2.59→45.86 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 1034 5.01 %
Rwork0.2052 --
obs0.2075 20634 91.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.59→45.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3646 0 44 2 3692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043771
X-RAY DIFFRACTIONf_angle_d0.6895143
X-RAY DIFFRACTIONf_dihedral_angle_d19.6031268
X-RAY DIFFRACTIONf_chiral_restr0.041593
X-RAY DIFFRACTIONf_plane_restr0.004663
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5901-2.72670.44271180.38972363X-RAY DIFFRACTION78
2.7267-2.89750.41541340.32642435X-RAY DIFFRACTION80
2.8975-3.12110.36591300.29482474X-RAY DIFFRACTION81
3.1211-3.43510.29921570.2493035X-RAY DIFFRACTION100
3.4351-3.9320.26121670.20653060X-RAY DIFFRACTION100
3.932-4.95290.2231630.17113087X-RAY DIFFRACTION100
4.9529-45.860.19581650.17723146X-RAY DIFFRACTION99
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)
16.61713.86640.34523.3306-2.59867.7308-0.10470.31550.75950.2693-0.120.74270.1090.14840.27920.64780.08010.08650.82610.14420.7962.3222114.338.9497
22.61220.4742-0.95422.73450.51112.87270.16690.21350.4903-0.30970.0627-0.17-0.23690.0156-0.23550.5103-0.0310.00370.48920.10730.572224.3819121.666529.3968
37.65053.2042-3.57578.992-1.55738.9680.1395-0.46910.71910.55280.1162-0.1619-0.21690.0691-0.31950.4876-0.1108-0.08740.4075-0.14240.725526.2985132.007138.3599
45.67882.0999-2.32037.4726-2.94694.60520.44230.06190.77150.2305-0.2809-0.5389-0.8768-0.2111-0.19950.6336-0.0769-0.05960.6013-0.11890.80227.8225131.287838.9852
53.36220.43421.01797.77386.23178.8248-0.2634-0.42130.3950.45550.842-0.9983-0.89340.4676-0.49770.6574-0.0528-0.29380.72440.02170.931343.6429122.660248.0769
63.3099-0.59682.52173.86810.45014.5213-0.6976-0.67350.49880.2321-0.3035-0.5992-0.8287-0.42040.86340.7526-0.1335-0.16180.7179-0.05990.953936.2167121.511253.7535
72.9019-0.51230.45392.79110.1755.0536-0.04150.30970.18210.17870.1267-0.08650.2542-0.2099-0.06120.411-0.0587-0.03080.51780.02330.53725.7206110.544636.0269
85.2368-0.17515.88241.6061-0.41318.45680.3058-0.0559-0.43720.51710.03560.0260.440.1295-0.40350.6177-0.0515-0.05810.64020.06990.543426.9781108.140355.5938
91.9201-1.04560.22822.5513-2.75793.1986-0.5458-0.31530.09931.5972-0.1859-0.2186-1.4994-0.11140.88951.2474-0.1652-0.10710.6245-0.0590.601339.6948124.22666.3861
103.3795-1.9984-1.19845.49211.63567.0995-0.2492-0.4569-0.08830.90320.2119-0.63441.05330.69360.04920.63330.0598-0.12210.59390.01540.525239.012389.198643.6773
112.1691.78430.71123.87071.78692.11260.0427-0.18550.62810.81260.3053-0.71830.22320.4631-0.36220.57930.0674-0.22070.7321-0.10270.878644.7954110.728647.3468
122.9894-0.20840.43883.4256-0.7543.6158-0.1680.35790.1656-0.15360.1334-0.05370.45940.17090.09520.48480.0248-0.05870.533-0.01760.613733.272397.632735.9621
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 106 )
3X-RAY DIFFRACTION3chain 'A' and (resid 107 through 128 )
4X-RAY DIFFRACTION4chain 'A' and (resid 129 through 157 )
5X-RAY DIFFRACTION5chain 'A' and (resid 158 through 174 )
6X-RAY DIFFRACTION6chain 'A' and (resid 175 through 201 )
7X-RAY DIFFRACTION7chain 'A' and (resid 202 through 236 )
8X-RAY DIFFRACTION8chain 'A' and (resid 237 through 284 )
9X-RAY DIFFRACTION9chain 'A' and (resid 285 through 326 )
10X-RAY DIFFRACTION10chain 'B' and (resid 82 through 196 )
11X-RAY DIFFRACTION11chain 'B' and (resid 197 through 249 )
12X-RAY DIFFRACTION12chain 'B' and (resid 250 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