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- PDB-4rxo: The structure of GTP-bound SAMHD1 -

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Basic information

Entry
Database: PDB / ID: 4rxo
TitleThe structure of GTP-bound SAMHD1
ComponentsDeoxynucleoside triphosphate triphosphohydrolase SAMHD1
KeywordsHYDROLASE / HD-domain / dNTP and GTP binding / phosphorylation
Function / homology
Function and homology information


Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / dGTP binding / dATP catabolic process / deoxyribonucleotide catabolic process / tetraspanin-enriched microdomain / dGTPase activity / dGTP catabolic process / DNA strand resection involved in replication fork processing ...Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / dGTP binding / dATP catabolic process / deoxyribonucleotide catabolic process / tetraspanin-enriched microdomain / dGTPase activity / dGTP catabolic process / DNA strand resection involved in replication fork processing / negative regulation of type I interferon-mediated signaling pathway / regulation of innate immune response / RNA nuclease activity / somatic hypermutation of immunoglobulin genes / double-strand break repair via homologous recombination / Interferon alpha/beta signaling / single-stranded DNA binding / site of double-strand break / protein homotetramerization / defense response to virus / nucleic acid binding / immune response / innate immune response / DNA damage response / GTP binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane
Similarity search - Function
Hypothetical protein af1432 / Hypothetical protein af1432 / : / HD domain profile. / HD domain / HD domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Metal dependent phosphohydrolases with conserved 'HD' motif. / Sterile alpha motif. ...Hypothetical protein af1432 / Hypothetical protein af1432 / : / HD domain profile. / HD domain / HD domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Metal dependent phosphohydrolases with conserved 'HD' motif. / Sterile alpha motif. / HD/PDEase domain / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsZhu, C.F. / Wei, W. / Peng, X. / Dong, Y.H. / Gong, Y. / Yu, X.F.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: The mechanism of substrate-controlled allosteric regulation of SAMHD1 activated by GTP.
Authors: Zhu, C.F. / Wei, W. / Peng, X. / Dong, Y.H. / Gong, Y. / Yu, X.F.
History
DepositionDec 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
B: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
C: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
D: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)252,67916
Polymers249,9454
Non-polymers2,73412
Water5,981332
1
A: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
B: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,3398
Polymers124,9722
Non-polymers1,3676
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-106 kcal/mol
Surface area37980 Å2
MethodPISA
2
C: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
D: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,3398
Polymers124,9722
Non-polymers1,3676
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-106 kcal/mol
Surface area37710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.219, 183.187, 81.275
Angle α, β, γ (deg.)90.00, 100.62, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 114 - 583 / Label seq-ID: 27 - 496

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 / dNTPase / Dendritic cell-derived IFNG-induced protein / DCIP / Monocyte protein 5 / MOP-5 / SAM ...dNTPase / Dendritic cell-derived IFNG-induced protein / DCIP / Monocyte protein 5 / MOP-5 / SAM domain and HD domain-containing protein 1


Mass: 62486.184 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SAMHD1, MOP5 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y3Z3, Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.26 Å3/Da / Density % sol: 45.59 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M sodium chloride, 0.1M Na/K phosphate, and 25% w/v polyethylene glycol 1000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 14, 2013
RadiationMonochromator: cryocooled channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 67543 / Num. obs: 65382 / % possible obs: 96.8 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 5.9 % / Biso Wilson estimate: 55.3 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 13.2
Reflection shellResolution: 2.6→2.64 Å / Rmerge(I) obs: 0.57 / % possible all: 93

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U1N

3u1n


Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.932 / SU B: 12.218 / SU ML: 0.246 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 1.172 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22203 3257 5 %RANDOM
Rwork0.18317 ---
obs0.18508 62523 96.64 %-
all-64697 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.699 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å20.39 Å2
2---5.16 Å20 Å2
3---5.6 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14493 0 152 332 14977
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01914990
X-RAY DIFFRACTIONr_bond_other_d0.0050.0214255
X-RAY DIFFRACTIONr_angle_refined_deg1.2591.96620252
X-RAY DIFFRACTIONr_angle_other_deg1.092332793
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.20951752
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.69623.757756
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.082152672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4515104
X-RAY DIFFRACTIONr_chiral_restr0.0680.22135
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02116678
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023578
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6136.287053
X-RAY DIFFRACTIONr_mcbond_other3.6116.2797052
X-RAY DIFFRACTIONr_mcangle_it5.9019.3968790
X-RAY DIFFRACTIONr_mcangle_other5.9019.3978791
X-RAY DIFFRACTIONr_scbond_it3.8686.7637937
X-RAY DIFFRACTIONr_scbond_other3.8566.7617921
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4479.95211437
X-RAY DIFFRACTIONr_long_range_B_refined9.20449.08817057
X-RAY DIFFRACTIONr_long_range_B_other9.20149.07917000
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A269420.12
12B269420.12
21A268410.12
22C268410.12
31A273680.12
32D273680.12
41B268610.11
42C268610.11
51B265650.12
52D265650.12
61C268360.12
62D268360.12
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 225 -
Rwork0.275 4328 -
obs--90.97 %

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