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- PDB-6yb9: Human octameric PAICS in complex with SAICAR, AMP-PNP, and magnesium -

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Basic information

Entry
Database: PDB / ID: 6yb9
TitleHuman octameric PAICS in complex with SAICAR, AMP-PNP, and magnesium
ComponentsMultifunctional protein ADE2
KeywordsBIOSYNTHETIC PROTEIN / de novo purine biosynthesis / nucleotide metabolism / cancer target
Function / homology
Function and homology information


phosphoribosylaminoimidazole carboxylase / 5-amino-4-imidazole carboxylate lyase activity / phosphoribosylaminoimidazole carboxylase activity / phosphoribosylaminoimidazolesuccinocarboxamide synthase / phosphoribosylaminoimidazolesuccinocarboxamide synthase activity / purine nucleobase biosynthetic process / 'de novo' XMP biosynthetic process / Purine ribonucleoside monophosphate biosynthesis / 'de novo' AMP biosynthetic process / GMP biosynthetic process ...phosphoribosylaminoimidazole carboxylase / 5-amino-4-imidazole carboxylate lyase activity / phosphoribosylaminoimidazole carboxylase activity / phosphoribosylaminoimidazolesuccinocarboxamide synthase / phosphoribosylaminoimidazolesuccinocarboxamide synthase activity / purine nucleobase biosynthetic process / 'de novo' XMP biosynthetic process / Purine ribonucleoside monophosphate biosynthesis / 'de novo' AMP biosynthetic process / GMP biosynthetic process / 'de novo' IMP biosynthetic process / cadherin binding / extracellular exosome / ATP binding / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Class II PurE / SAICAR synthetase signature 1. / SAICAR synthetase signature 2. / SAICAR synthetase, conserved site / SAICAR synthetase/ADE2, N-terminal / SAICAR synthetase / PurE domain / AIR carboxylase / AIR carboxylase / Rossmann fold - #1970 ...Class II PurE / SAICAR synthetase signature 1. / SAICAR synthetase signature 2. / SAICAR synthetase, conserved site / SAICAR synthetase/ADE2, N-terminal / SAICAR synthetase / PurE domain / AIR carboxylase / AIR carboxylase / Rossmann fold - #1970 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-OK8 / Bifunctional phosphoribosylaminoimidazole carboxylase/phosphoribosylaminoimidazole succinocarboxamide synthetase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.406 Å
AuthorsSkerlova, J. / Unterlass, J. / Gottmann, M. / Homan, E. / Helleday, T. / Jemth, A.S. / Stenmark, P.
Funding support Sweden, European Union, Czech Republic, 3items
OrganizationGrant numberCountry
Swedish Research Council Sweden
European Research Council (ERC)695376European Union
Ministry of Education (MoE, Czech Republic)CZ.02.2.69/0.0/0.0/16_027/0008477 Czech Republic
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Crystal structures of human PAICS reveal substrate and product binding of an emerging cancer target.
Authors: Skerlova, J. / Unterlass, J. / Gottmann, M. / Marttila, P. / Homan, E. / Helleday, T. / Jemth, A.S. / Stenmark, P.
History
DepositionMar 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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 / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.2Jan 24, 2024Group: Data collection / Database references / 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Multifunctional protein ADE2
B: Multifunctional protein ADE2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,66116
Polymers94,2702
Non-polymers2,39114
Water5,152286
1
A: Multifunctional protein ADE2
B: Multifunctional protein ADE2
hetero molecules

A: Multifunctional protein ADE2
B: Multifunctional protein ADE2
hetero molecules

A: Multifunctional protein ADE2
B: Multifunctional protein ADE2
hetero molecules

A: Multifunctional protein ADE2
B: Multifunctional protein ADE2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)386,64364
Polymers377,0818
Non-polymers9,56256
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area55070 Å2
ΔGint-280 kcal/mol
Surface area118610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.263, 154.019, 223.624
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 7 - 425 / Label seq-ID: 7 - 425

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Multifunctional protein ADE2


Mass: 47135.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAICS, ADE2, AIRC, PAIS / Production host: Escherichia coli (E. coli)
References: UniProt: P22234, phosphoribosylaminoimidazolesuccinocarboxamide synthase, phosphoribosylaminoimidazole carboxylase

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Non-polymers , 5 types, 300 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-OK8 / (2~{S})-2-[[5-azanyl-1-[(2~{R},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]imidazol-4-yl]car bonylamino]butanedioic acid / SAICAR


Mass: 454.283 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H19N4O12P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.8 Å3/Da / Density % sol: 56.04 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 6 mg/ml PAICS with 5 mM SAICAR, 5 mM AMP-PNP, and 10 mM MgCl2; 0.1 M MES/imidazole pH 6.5, 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M ...Details: 6 mg/ml PAICS with 5 mM SAICAR, 5 mM AMP-PNP, and 10 mM MgCl2; 0.1 M MES/imidazole pH 6.5, 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, and 0.02 M sodium oxamate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.406→47.33 Å / Num. obs: 41224 / % possible obs: 99 % / Redundancy: 10.876 % / Biso Wilson estimate: 39.747 Å2 / CC1/2: 0.966 / Rmerge(I) obs: 0.336 / Rrim(I) all: 0.353 / Χ2: 0.987 / Net I/σ(I): 5.16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.406-2.5510.8631.0491.8265310.7241.198.7
2.55-2.7310.9280.8242.462350.8340.86499.9
2.73-2.9410.8310.6153.2857930.8860.64599.9
2.94-3.2210.8280.4584.3553910.9220.48199.8
3.22-3.611.0710.3366.2648610.9590.35299.7
3.6-4.1611.0580.278.3142890.9510.28399.1
4.16-5.0810.9480.2479.5336490.9590.25998.5
5.08-7.1410.7260.258.6828310.9540.26397.4
7.14-47.3310.1020.21410.8416440.9630.22594.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0232refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2h31

2h31


Resolution: 2.406→47.33 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.919 / SU R Cruickshank DPI: 0.3412 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.341 / ESU R Free: 0.237
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2293 2061 5 %RANDOM
Rwork0.177 ---
obs0.1796 39161 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 144.47 Å2 / Biso mean: 39.167 Å2 / Biso min: 19.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2--2.78 Å20 Å2
3----2.59 Å2
Refinement stepCycle: final / Resolution: 2.406→47.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6528 0 150 286 6964
Biso mean--48.59 38.72 -
Num. residues----838
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0136808
X-RAY DIFFRACTIONr_bond_other_d0.0350.0176374
X-RAY DIFFRACTIONr_angle_refined_deg1.5851.6519220
X-RAY DIFFRACTIONr_angle_other_deg2.3281.58114868
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.275836
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6323.419310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.315151208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6151532
X-RAY DIFFRACTIONr_chiral_restr0.0720.2894
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027436
X-RAY DIFFRACTIONr_gen_planes_other0.0110.021320
Refine LS restraints NCS

Ens-ID: 1 / Number: 12954 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.406→2.468 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.336 146 -
Rwork0.279 2788 -
obs--97.22 %

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