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- PDB-3r3m: Crystal structure of the FAF1 UBX domain -

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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


Fas signaling pathway / ooplasm / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / CD95 death-inducing signaling complex / 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 ...Fas signaling pathway / ooplasm / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / CD95 death-inducing signaling complex / 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 / ERAD pathway / negative regulation of canonical NF-kappaB signal transduction / positive regulation of DNA replication / ubiquitin binding / 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-like, UBX domain / FAF1, UBA-like domain / : / Fas-associated factor 1 / UAS / : / UAS / Domain present in ubiquitin-regulatory proteins / UBX domain / UBX domain ...FAS-associated factor 1-like, UBX domain / FAF1, UBA-like domain / : / Fas-associated factor 1 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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


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


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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

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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

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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

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