[English] 日本語
Yorodumi
- PDB-3qnu: Crystal structure of the cytosolic domain of human atlastin-1 in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qnu
TitleCrystal structure of the cytosolic domain of human atlastin-1 in complex with GDP, hexagonal form
ComponentsAtlastin-1
KeywordsHYDROLASE / GTPase / homotypic fusion / Ras-like GTPase / membrane fusion / GDP / GTP / endopalsmic reticulum
Function / homology
Function and homology information


endoplasmic reticulum tubular network membrane organization / endoplasmic reticulum tubular network membrane / Golgi cis cisterna / endoplasmic reticulum tubular network / endoplasmic reticulum organization / axonogenesis / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein homooligomerization / Golgi membrane / axon ...endoplasmic reticulum tubular network membrane organization / endoplasmic reticulum tubular network membrane / Golgi cis cisterna / endoplasmic reticulum tubular network / endoplasmic reticulum organization / axonogenesis / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein homooligomerization / Golgi membrane / axon / GTPase activity / endoplasmic reticulum membrane / GTP binding / Golgi apparatus / endoplasmic reticulum / identical protein binding / membrane
Similarity search - Function
AHSP / Guanylate-binding protein, N-terminal / Guanylate-binding protein, C-terminal domain superfamily / Guanylate-binding protein, N-terminal domain / GB1/RHD3-type guanine nucleotide-binding (G) domain / GB1/RHD3-type guanine nucleotide-binding (G) domain profile. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold ...AHSP / Guanylate-binding protein, N-terminal / Guanylate-binding protein, C-terminal domain superfamily / Guanylate-binding protein, N-terminal domain / GB1/RHD3-type guanine nucleotide-binding (G) domain / GB1/RHD3-type guanine nucleotide-binding (G) domain profile. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Atlastin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsLiu, X.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structures of the atlastin GTPase provide insight into homotypic fusion of endoplasmic reticulum membranes.
Authors: Bian, X. / Klemm, R.W. / Liu, T.Y. / Zhang, M. / Sun, S. / Sui, X. / Liu, X. / Rapoport, T.A. / Hu, J.
History
DepositionFeb 9, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Atlastin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1863
Polymers52,7191
Non-polymers4682
Water36020
1
A: Atlastin-1
hetero molecules

A: Atlastin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,3726
Polymers105,4372
Non-polymers9354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area4360 Å2
ΔGint-20 kcal/mol
Surface area35610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.889, 144.889, 103.694
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-465-

HOH

-
Components

#1: Protein Atlastin-1 / Brain-specific GTP-binding protein / GTP-binding protein 3 / GBP-3 / hGBP3 / Guanine nucleotide- ...Brain-specific GTP-binding protein / GTP-binding protein 3 / GBP-3 / hGBP3 / Guanine nucleotide-binding protein 3 / Spastic paraplegia 3 protein A


Mass: 52718.609 Da / Num. of mol.: 1 / Fragment: atlastin ecto-domain (UNP RESIDUES 18-447)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATL1, GBP3, SPG3A / Plasmid: Pet30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8WXF7, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl, pH8.5, 25%(w/v) PEG1500, 20%(v/v) Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793, 0.9795
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 14, 2010 / Details: mirrors
RadiationMonochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97951
ReflectionResolution: 2.8→40 Å / Num. all: 16311 / Num. obs: 16292 / % possible obs: 99.88 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 13.6 % / Biso Wilson estimate: 67.8 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 14.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
2.8-3.0290.336.430150.3399.9
3.02-3.32130.151931600.15100
3.32-3.8150.073832580.07100
3.8-4.79160.045533130.04100
4.79-50150.0412234900.04100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.8→39.966 Å / SU ML: 0.37 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): 0 / Stereochemistry target values: ML / Details: Used weighted full matrix least squares procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.3061 823 5.05 %RANDOM
Rwork0.2352 ---
all0.2644 16311 --
obs0.2385 16292 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.648 Å2 / ksol: 0.314 e/Å3
Displacement parametersBiso mean: 71.58 Å2
Baniso -1Baniso -2Baniso -3
1--1.5249 Å20 Å2-0 Å2
2---1.5249 Å20 Å2
3----19.7086 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.039 Å0.03 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.8→39.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3050 0 29 20 3099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113142
X-RAY DIFFRACTIONf_angle_d1.4664259
X-RAY DIFFRACTIONf_dihedral_angle_d21.4991124
X-RAY DIFFRACTIONf_chiral_restr0.094474
X-RAY DIFFRACTIONf_plane_restr0.005546
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection obs
2.8-2.97540.34061310.263725220.0132757
2.9754-3.20510.33281600.267124990.0132591
3.2051-3.52740.32441140.250825520.0142548
3.5274-4.03740.29021560.2325480.0122552
4.0374-5.08510.25281360.20225910.0122499
5.0851-39.97010.32621260.235227570.0132522

+
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