[English] 日本語
Yorodumi
- PDB-7rk3: Crystal structure of human N-myristoyltransferase 1 fragment (res... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rk3
TitleCrystal structure of human N-myristoyltransferase 1 fragment (residues 109-496) bound to diacylated human Arf6 octapeptide and Coenzyme A
Components
  • ADP-ribosylation factor 6
  • Glycylpeptide N-tetradecanoyltransferase 1
KeywordsTRANSFERASE
Function / homology
Function and homology information


erythrocyte apoptotic process / maintenance of postsynaptic density structure / protein localization to cleavage furrow / myristoyltransferase activity / N-terminal peptidyl-glycine N-myristoylation / peptidyl-lysine N6-myristoyltransferase activity / Late Phase of HIV Life Cycle / ketone metabolic process / positive regulation of mitotic cytokinetic process / regulation of opsin-mediated signaling pathway ...erythrocyte apoptotic process / maintenance of postsynaptic density structure / protein localization to cleavage furrow / myristoyltransferase activity / N-terminal peptidyl-glycine N-myristoylation / peptidyl-lysine N6-myristoyltransferase activity / Late Phase of HIV Life Cycle / ketone metabolic process / positive regulation of mitotic cytokinetic process / regulation of opsin-mediated signaling pathway / negative regulation of dendrite development / Activation, myristolyation of BID and translocation to mitochondria / positive regulation of establishment of protein localization to mitochondrion / regulation of dendritic spine development / regulation of Rac protein signal transduction / negative regulation of protein localization to cell surface / establishment of epithelial cell polarity / protein localization to endosome / negative regulation of receptor-mediated endocytosis / ruffle assembly / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / regulation of filopodium assembly / endocytic recycling / MET receptor recycling / thioesterase binding / Flemming body / protein localization to cell surface / filopodium membrane / protein localization to membrane / TBC/RABGAPs / cortical actin cytoskeleton organization / positive regulation of actin filament polymerization / hepatocyte apoptotic process / cleavage furrow / synaptic vesicle endocytosis / regulation of presynapse assembly / endocytic vesicle / eNOS activation / vesicle-mediated transport / ruffle / signaling adaptor activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / liver development / small monomeric GTPase / protein localization to plasma membrane / positive regulation of protein secretion / positive regulation of protein localization to plasma membrane / intracellular protein transport / cellular response to nerve growth factor stimulus / positive regulation of neuron projection development / recycling endosome membrane / GDP binding / Inactivation, recovery and regulation of the phototransduction cascade / Clathrin-mediated endocytosis / presynapse / G protein activity / nervous system development / early endosome membrane / cell cortex / midbody / in utero embryonic development / cell differentiation / postsynapse / endosome / cell adhesion / cell division / focal adhesion / GTPase activity / GTP binding / glutamatergic synapse / Golgi apparatus / extracellular exosome / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
ADP-ribosylation factor 6 / Glycylpeptide N-tetradecanoyltransferase, conserved site / Myristoyl-CoA:protein N-myristoyltransferase signature 1. / Myristoyl-CoA:protein N-myristoyltransferase signature 2. / Glycylpeptide N-tetradecanoyltransferase / Glycylpeptide N-tetradecanoyltransferase, N-terminal / Glycylpeptide N-tetradecanoyltransferase, C-terminal / Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain / Myristoyl-CoA:protein N-myristoyltransferase, C-terminal domain / Small GTPase superfamily, ARF type ...ADP-ribosylation factor 6 / Glycylpeptide N-tetradecanoyltransferase, conserved site / Myristoyl-CoA:protein N-myristoyltransferase signature 1. / Myristoyl-CoA:protein N-myristoyltransferase signature 2. / Glycylpeptide N-tetradecanoyltransferase / Glycylpeptide N-tetradecanoyltransferase, N-terminal / Glycylpeptide N-tetradecanoyltransferase, C-terminal / Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain / Myristoyl-CoA:protein N-myristoyltransferase, C-terminal domain / Small GTPase superfamily, ARF type / small GTPase Arf family profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Acyl-CoA N-acyltransferase / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
4'-diphospho pantetheine / HEXANOIC ACID / MYRISTIC ACID / Glycylpeptide N-tetradecanoyltransferase 1 / ADP-ribosylation factor 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsFenwick, M.K. / Lin, H.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK107868-04 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124165-01 United States
National Institutes of Health/Office of the DirectorS10OD021527
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: To Be Published
Title: Crystal structure of human N-myristoyltransferase 1 fragment (residues 109-496) bound to diacylated human Arf6 octapeptide and Coenzyme A
Authors: Fenwick, M.K. / Lin, H.
History
DepositionJul 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycylpeptide N-tetradecanoyltransferase 1
B: ADP-ribosylation factor 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1295
Polymers46,3462
Non-polymers7833
Water7,927440
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-3 kcal/mol
Surface area15820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.984, 76.046, 106.342
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Glycylpeptide N-tetradecanoyltransferase 1 / Myristoyl-CoA:protein N-myristoyltransferase 1 / Type I N-myristoyltransferase / Peptide N- ...Myristoyl-CoA:protein N-myristoyltransferase 1 / Type I N-myristoyltransferase / Peptide N-myristoyltransferase 1


Mass: 45453.348 Da / Num. of mol.: 1 / Fragment: UNP residues 29-416
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NMT1, NMT / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P30419, glycylpeptide N-tetradecanoyltransferase
#2: Protein/peptide ADP-ribosylation factor 6


Mass: 893.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARF6 / Production host: unidentified (others) / References: UniProt: P62330

-
Non-polymers , 4 types, 443 molecules

#3: Chemical ChemComp-4PS / 4'-diphospho pantetheine / N~3~-[(2R)-2-hydroxy-4-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}-3,3-dimethylbutanoyl]-N-(2-sulfanylethyl)-beta-alaninamide


Mass: 438.328 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24N2O10P2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-6NA / HEXANOIC ACID


Mass: 116.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 20% (w/v) PEG 3350, 200mM ammonium formate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.05→106.34 Å / Num. obs: 24871 / % possible obs: 99 % / Redundancy: 3.6 % / Biso Wilson estimate: 28.34 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.04 / Rrim(I) all: 0.078 / Net I/σ(I): 13.1 / Num. measured all: 88647
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.05-2.113.10.475573918330.860.310.5712.196.1
8.93-106.343.20.015120137510.010.01843.899.9

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
PHENIX1.19.1_4122phasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HsNMT1

Resolution: 2.05→61.86 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 26.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2197 1216 4.9 %
Rwork0.1585 23576 -
obs0.1616 24792 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.44 Å2 / Biso mean: 34.6862 Å2 / Biso min: 17.82 Å2
Refinement stepCycle: final / Resolution: 2.05→61.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2955 0 48 442 3445
Biso mean--38.63 43.52 -
Num. residues----360
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.130.3081380.27752483262196
2.13-2.230.28941180.22692605272399
2.23-2.350.28361350.19922576271199
2.35-2.490.26821540.17352590274499
2.49-2.690.3041350.17692568270398
2.69-2.960.2511180.17282645276399
2.96-3.380.23241360.14772637277399
3.38-4.260.15731230.1262680280399
4.26-61.860.17181590.13362792295199
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)
11.5783-0.67510.1691.33490.10322.79190.006-0.1244-0.07620.01110.0419-0.0550.07050.1328-0.04340.2319-0.023-0.01770.20490.01720.211212.5357-2.71957.4577
26.4641-4.4023-0.8155.22710.11212.2907-0.0711-0.09750.19670.27480.0533-0.20010.1625-0.1320.00760.1741-0.063-0.01040.22120.01380.13363.6075-6.55838.8748
30.58190.0866-0.02020.6436-0.24252.9912-0.0345-0.0794-0.0496-0.02720.02540.02140.2342-0.15290.01120.2597-0.0106-0.01630.2090.00920.25311.047-7.46322.594
48.78752.70086.08668.79174.45119.36730.0292-0.0563-0.1669-0.1753-0.13270.3201-0.0439-0.42040.12860.2898-0.05450.05210.2109-0.05760.23163.0093-13.1822-27.9697
50.6622-0.29320.3081.8293-0.92932.4235-0.0552-0.01690.09880.10510.1120.0211-0.3915-0.1038-0.05410.29240.0183-0.00360.24380.00460.2368-2.712911.4524-8.8911
61.39160.1385-0.19541.4544-0.41913.02780.00820.0268-0.11-0.11990.06140.10860.095-0.1799-0.07020.2651-0.0156-0.01680.18780.01430.2297-3.2951-1.9662-10.0672
77.3372-2.2373-0.76033.616-2.61923.2345-0.41680.1074-0.3962-0.57040.37240.5155-0.6964-0.17950.00010.2866-0.0705-0.01920.22450.03870.27262.3399-12.1743-9.5551
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 145 through 235 )A145 - 235
2X-RAY DIFFRACTION2chain 'A' and (resid 236 through 259 )A236 - 259
3X-RAY DIFFRACTION3chain 'A' and (resid 260 through 308 )A260 - 308
4X-RAY DIFFRACTION4chain 'A' and (resid 309 through 326 )A309 - 326
5X-RAY DIFFRACTION5chain 'A' and (resid 327 through 407 )A327 - 407
6X-RAY DIFFRACTION6chain 'A' and (resid 408 through 496 )A408 - 496
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 9 )B2 - 9

+
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