[English] 日本語
Yorodumi
- PDB-1tr8: Crystal Structure of archaeal Nascent Polypeptide-associated Comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tr8
TitleCrystal Structure of archaeal Nascent Polypeptide-associated Complex (aeNAC)
Componentsconserved protein (MTH177)
KeywordsCHAPERONE / Chaperones / Nascent Polypeptide-associated Complex / Ribosome / UBA-domain / Ubiquitin
Function / homology
Function and homology information


nascent polypeptide-associated complex / protein transport / RNA binding
Similarity search - Function
Nascent polypeptide-associated complex (NAC), archaeal / Nascent polypeptide-associated complex domain / Nascent polypeptide-associated complex NAC domain / Nascent polypeptide-associated complex subunit alpha / NAC A/B domain superfamily / NAC domain / NAC A/B domain profile. / NAC / Nascent polypeptide-associated complex subunit alpha-like, UBA domain / HYPK UBA domain ...Nascent polypeptide-associated complex (NAC), archaeal / Nascent polypeptide-associated complex domain / Nascent polypeptide-associated complex NAC domain / Nascent polypeptide-associated complex subunit alpha / NAC A/B domain superfamily / NAC domain / NAC A/B domain profile. / NAC / Nascent polypeptide-associated complex subunit alpha-like, UBA domain / HYPK UBA domain / Ubiquitin Ligase Nedd4; Chain: W; / Ubiquitin-associated (UBA) domain / UBA-like superfamily / Single Sheet / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Nascent polypeptide-associated complex protein
Similarity search - Component
Biological speciesMethanothermobacter marburgensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.27 Å
AuthorsSpreter, T. / Pech, M. / Beatrix, B.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: The crystal structure of archaeal nascent polypeptide-associated complex (NAC) reveals a unique fold and the presence of a UBA domain
Authors: Spreter, T. / Pech, M. / Beatrix, B.
History
DepositionJun 21, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: conserved protein (MTH177)
B: conserved protein (MTH177)


Theoretical massNumber of molelcules
Total (without water)23,9292
Polymers23,9292
Non-polymers00
Water75742
1
A: conserved protein (MTH177)
B: conserved protein (MTH177)

A: conserved protein (MTH177)
B: conserved protein (MTH177)


Theoretical massNumber of molelcules
Total (without water)47,8584
Polymers47,8584
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_667-y+1,-x+1,-z+5/21
Unit cell
Length a, b, c (Å)90.89, 90.89, 49.476
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSGLUAA27 - 7012 - 55
21LYSGLUBB27 - 7012 - 55
12ILEARGAA79 - 11564 - 100
22ILEARGBB79 - 11564 - 100

NCS ensembles :
ID
1
2
DetailsThe biological unit is a homodimer. The two monomers in the asymetric unit belong to two different homodimers. Each biological unit is assembled by the crystal symmetry.

-
Components

#1: Protein conserved protein (MTH177) / delta1-18 Archaeal Nascent Polypeptide Associated Complex


Mass: 11964.399 Da / Num. of mol.: 2 / Fragment: N-terminal truncated aeNAC (aminoacids 19-117)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter marburgensis (archaea)
Gene: MTH177 (amonoacids 19-117) / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: P0C0K9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7
Details: sodium malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9795, 0.9797, 0.9117, 0.99
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 14, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97971
30.91171
40.991
ReflectionResolution: 2.27→20 Å / Num. all: 9416 / Num. obs: 8963 / % possible obs: 96.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.2 % / Biso Wilson estimate: 56.5 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 8.5
Reflection shellResolution: 2.27→2.39 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.168 / Mean I/σ(I) obs: 4 / Rsym value: 0.168 / % possible all: 96.4

-
Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHENIX(HYSS)phasing
SHARPphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.27→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.923 / SU B: 12.873 / SU ML: 0.171 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 4 / ESU R: 0.323 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24043 453 4.8 %RANDOM
Rwork0.1937 ---
all0.196 9416 --
obs0.19587 8963 94.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 57.007 Å2
Baniso -1Baniso -2Baniso -3
1-1.81 Å20 Å20 Å2
2--1.81 Å20 Å2
3----3.63 Å2
Refinement stepCycle: LAST / Resolution: 2.27→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1452 0 0 42 1494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221458
X-RAY DIFFRACTIONr_bond_other_d0.0010.021408
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.9881946
X-RAY DIFFRACTIONr_angle_other_deg0.67633288
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6965182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.85625.42970
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.18615316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9911514
X-RAY DIFFRACTIONr_chiral_restr0.0730.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021586
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02252
X-RAY DIFFRACTIONr_nbd_refined0.2210.2208
X-RAY DIFFRACTIONr_nbd_other0.220.21235
X-RAY DIFFRACTIONr_nbtor_other0.0890.2935
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.247
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0380.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3730.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2970.2101
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.27
X-RAY DIFFRACTIONr_mcbond_it1.4891.51113
X-RAY DIFFRACTIONr_mcbond_other0.251.5380
X-RAY DIFFRACTIONr_mcangle_it1.59321466
X-RAY DIFFRACTIONr_scbond_it2.9033578
X-RAY DIFFRACTIONr_scangle_it4.4614.5480
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1260tight positional0.080.05
2218tight positional0.070.05
1460medium positional0.820.5
2317medium positional0.710.5
1260tight thermal0.190.5
2218tight thermal0.210.5
1460medium thermal0.712
2317medium thermal0.922
LS refinement shellResolution: 2.272→2.331 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.265 48
Rwork0.217 554
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
16.18351.46195.31173.14052.35579.3886-0.07350.3274-0.1666-0.28610.1562-0.20940.11030.2483-0.0827-0.1399-0.02830.0243-0.09050.0299-0.119484.13624.06460.296
24.3505-1.6234-1.62055.35681.221511.57580.06160.0290.1151-0.1056-0.1110.0642-0.39040.02730.0493-0.1233-0.0431-0.0254-0.13770.0391-0.099964.37912.22661.461
325.2038-13.7691-13.752515.12568.126315.54610.0373-0.60230.89570.3579-0.06040.2711-0.4014-0.11060.02310.09490.0291-0.0515-0.0573-0.060.099780.44836.97871.489
414.802616.4506-9.905618.5753-10.98456.63061.3861-0.8187-1.16124.1545-0.58690.98720.1682-0.6868-0.79920.7561-0.16210.03130.09850.05650.457558.144-0.43871.599
51.06531.40674.47297.335310.278722.2705-0.25360.39380.5426-0.59740.0682-0.0478-0.32760.93630.1854-0.13750.0027-0.0026-0.04660.0334-0.013385.27924.28355.093
64.86762.32520.29722.7614-1.389310.4217-0.56440.654-0.0975-0.12210.18980.3148-0.5331-0.73520.3746-0.0889-0.042-0.0016-0.11540.012-0.040564.11313.11256.038
79.147-5.0491-0.022311.4523-2.56047.4897-0.12130.13960.06680.2363-0.22920.35030.20880.26540.3505-0.2465-0.0561-0.0317-0.08180.0079-0.088359.89516.82734.871
810.1194-0.07383.43052.2957-1.129221.4211-0.1584-0.34630.08010.3138-0.4563-0.23970.84350.83740.6147-0.1552-0.03030.0524-0.06650.0860.008790.11820.75333.43
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA26 - 5311 - 38
2X-RAY DIFFRACTION2BB26 - 5311 - 38
3X-RAY DIFFRACTION3AA54 - 6139 - 46
4X-RAY DIFFRACTION4BB54 - 6139 - 46
5X-RAY DIFFRACTION5AA62 - 7247 - 57
6X-RAY DIFFRACTION6BB62 - 7247 - 57
7X-RAY DIFFRACTION7AA80 - 11565 - 100
8X-RAY DIFFRACTION8BB80 - 11565 - 100

+
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://pdbjlvh1.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