[English] 日本語
Yorodumi
- PDB-3r3m: Crystal structure of the FAF1 UBX domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3r3m
TitleCrystal structure of the FAF1 UBX domain
ComponentsFAS-associated factor 1
KeywordsAPOPTOSIS / beta grasp fold / p97 / phosphorylation
Function / homology
Function and homology information


ooplasm / CD95 death-inducing signaling complex / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / cytoplasmic sequestering of NF-kappaB / protein kinase regulator activity / VCP-NPL4-UFD1 AAA ATPase complex / regulation of protein catabolic process / NF-kappaB binding / regulation of cell adhesion / : ...ooplasm / CD95 death-inducing signaling complex / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / cytoplasmic sequestering of NF-kappaB / protein kinase regulator activity / VCP-NPL4-UFD1 AAA ATPase complex / regulation of protein catabolic process / NF-kappaB binding / regulation of cell adhesion / : / heat shock protein binding / positive regulation of DNA replication / ubiquitin binding / positive regulation of protein-containing complex assembly / positive regulation of protein catabolic process / nuclear envelope / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of apoptotic process / protein domain specific binding / apoptotic process / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / endoplasmic reticulum / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / Fas-associated factor 1 / FAS-associated factor 1-like, UBX domain / FAF1, UBA-like domain / UAS / UAS / Domain present in ubiquitin-regulatory proteins / UBX domain / UBX domain / UBX domain profile. ...: / Fas-associated factor 1 / FAS-associated factor 1-like, UBX domain / FAF1, UBA-like domain / UAS / UAS / Domain present in ubiquitin-regulatory proteins / UBX domain / UBX domain / UBX domain profile. / UBA-like domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Thioredoxin-like superfamily / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / FAS-associated factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHaenzelmann, P. / Schindelin, H.
CitationJournal: Structure / Year: 2011
Title: Hierarchical Binding of Cofactors to the AAA ATPase p97.
Authors: Hanzelmann, P. / Buchberger, A. / Schindelin, H.
History
DepositionMar 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / 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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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
B: FAS-associated factor 1
A: FAS-associated factor 1
C: FAS-associated factor 1
D: FAS-associated factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0757
Polymers39,7904
Non-polymers2853
Water43224
1
A: FAS-associated factor 1


Theoretical massNumber of molelcules
Total (without water)9,9471
Polymers9,9471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FAS-associated factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1373
Polymers9,9471
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: FAS-associated factor 1


Theoretical massNumber of molelcules
Total (without water)9,9471
Polymers9,9471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: FAS-associated factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0422
Polymers9,9471
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.755, 92.755, 108.500
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
31C
41D

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUTHRTHRchain B and (resseq 571:618 or resseq 621:649 )BA571 - 6186 - 53
12ARGARGLYSLYSchain B and (resseq 571:618 or resseq 621:649 )BA621 - 64956 - 84
21GLUGLUTHRTHRchain A and (resseq 571:618 or resseq 621:649 )AB571 - 6186 - 53
22ARGARGLYSLYSchain A and (resseq 571:618 or resseq 621:649 )AB621 - 64956 - 84
31GLUGLUTHRTHRchain C and (resseq 571:618 or resseq 621:649 )CC571 - 6186 - 53
32ARGARGLYSLYSchain C and (resseq 571:618 or resseq 621:649 )CC621 - 64956 - 84
41GLUGLUTHRTHRchain D and (resseq 571:618 or resseq 621:649 )DD571 - 6186 - 53
42ARGARGLYSLYSchain D and (resseq 571:618 or resseq 621:649 )DD621 - 64956 - 84

-
Components

#1: Protein
FAS-associated factor 1 / hFAF1 / UBX domain-containing protein 12 / UBX domain-containing protein 3A


Mass: 9947.401 Da / Num. of mol.: 4 / Fragment: unp residues 568-650
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAF1, UBXD12, UBXN3A, CGI-03 / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UNN5
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 3.43 Å3/Da / Density % sol: 64.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.4 M NaH2PO4/1.6 M K2HPO4, 0.1 M imidazole, 0.2 M NaCl, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 6, 2011
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3→80.34 Å / Num. all: 10693 / Num. obs: 10693 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 12.5
Reflection shellResolution: 3→3.16 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1559 / Rsym value: 0.518 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
PHENIX1.6.2_432refinement
PDB_EXTRACT3.1data extraction
MxCuBEdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3QQ8

3qq8


Resolution: 3→42.645 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.43 / σ(F): 0 / Phase error: 24.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2578 498 4.79 %random
Rwork0.1743 ---
all0.1782 10402 --
obs0.1782 10402 97.58 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.417 Å2 / ksol: 0.365 e/Å3
Displacement parametersBiso max: 198.21 Å2 / Biso mean: 54.3095 Å2 / Biso min: 9.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.6734 Å20 Å2-0 Å2
2--0.6734 Å20 Å2
3----1.3467 Å2
Refinement stepCycle: LAST / Resolution: 3→42.645 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2724 0 15 24 2763
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_deg1.324
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B640X-RAY DIFFRACTIONPOSITIONAL1.002
12A640X-RAY DIFFRACTIONPOSITIONAL1.002
13C640X-RAY DIFFRACTIONPOSITIONAL1.128
14D640X-RAY DIFFRACTIONPOSITIONAL0.919
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)
12.26941.2612-0.99245.2613-1.96840.93880.0633-0.02150.34050.83690.36250.1332-0.3373-0.2041-0.21540.17950.02780.00580.17670.03030.0867-36.403413.54032.818
20.82950.1188-0.43841.63480.33630.372-0.03690.3357-0.1547-0.39590.10790.014-0.0502-0.2009-0.08010.108-0.0375-0.00540.2372-0.01410.1167-38.387416.8059-23.9131
32.05561.1834-1.09241.2603-1.00871.6238-0.3172-0.2084-0.70270.032-0.2505-0.49610.01690.58950.54520.0748-0.00720.03870.21990.18880.3474-15.217312.7684-8.4262
41.48740.1948-2.0031.996-0.64514.72540.23510.36380.14350.2864-0.1927-0.2119-1.1429-0.9677-0.01090.46270.1793-0.06460.2720.02530.0636-42.22938.3038-11.1458
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 566:649)A566 - 649
2X-RAY DIFFRACTION2(chain B and resid 568:649)B568 - 649
3X-RAY DIFFRACTION3(chain C and resid 569:649)C569 - 649
4X-RAY DIFFRACTION4(chain D and resid 567:649)D567 - 649

+
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