[English] 日本語
Yorodumi
- PDB-4cc9: Crystal structure of human SAMHD1 (amino acid residues 582-626) b... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4cc9
TitleCrystal structure of human SAMHD1 (amino acid residues 582-626) bound to Vpx isolated from sooty mangabey and human DCAF1 (amino acid residues 1058-1396)
Components
  • DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1
  • PROTEIN VPRBP
  • PROTEIN VPX
KeywordsPROTEIN BINDING / HIV / SIV / RETROVIRAL RESTRICTION FACTOR / RETROVIRAL ACCESSORY PROTEIN / UBIQUITINATION / PROTEASOMAL DEGRADATION
Function / homology
Function and homology information


histone H2AT120 kinase activity / cell competition in a multicellular organism / Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / triphosphoric monoester hydrolase activity / dGTP binding / dATP catabolic process / dGTPase activity / : ...histone H2AT120 kinase activity / cell competition in a multicellular organism / Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / triphosphoric monoester hydrolase activity / dGTP binding / dATP catabolic process / dGTPase activity / : / tetraspanin-enriched microdomain / virion component => GO:0044423 / DNA strand resection involved in replication fork processing / deoxyribonucleotide catabolic process / dGTP catabolic process / V(D)J recombination / Cul4-RING E3 ubiquitin ligase complex / negative regulation of type I interferon-mediated signaling pathway / regulation of innate immune response / ubiquitin-like ligase-substrate adaptor activity / somatic hypermutation of immunoglobulin genes / RNA nuclease activity / viral life cycle / B cell differentiation / post-translational protein modification / nuclear estrogen receptor binding / double-strand break repair via homologous recombination / fibrillar center / positive regulation of protein catabolic process / Interferon alpha/beta signaling / Antigen processing: Ubiquitination & Proteasome degradation / site of double-strand break / single-stranded DNA binding / protein homotetramerization / defense response to virus / nucleic acid binding / non-specific serine/threonine protein kinase / protein ubiquitination / immune response / phosphorylation / protein serine kinase activity / innate immune response / DNA damage response / host cell nucleus / GTP binding / negative regulation of transcription by RNA polymerase II / RNA binding / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / metal ion binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4730 / Retroviral VpR/VpX protein / VPR/VPX protein / VPRBP/DCAF1 family / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / HD domain profile. / HD domain / HD domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4730 / Retroviral VpR/VpX protein / VPR/VPX protein / VPRBP/DCAF1 family / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / HD domain profile. / HD domain / HD domain / SAM domain (Sterile alpha motif) / YVTN repeat-like/Quinoprotein amine dehydrogenase / SAM domain profile. / Sterile alpha motif. / Metal dependent phosphohydrolases with conserved 'HD' motif. / Sterile alpha motif domain / HD/PDEase domain / 7 Propeller / Methylamine Dehydrogenase; Chain H / Sterile alpha motif/pointed domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Armadillo-like helical / Armadillo-type fold / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Protein Vpx / Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 / DDB1- and CUL4-associated factor 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SIMIAN IMMUNODEFICIENCY VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.473 Å
AuthorsSchwefel, D. / Groom, H.C.T. / Boucherit, V.C. / Christodoulou, E. / Walker, P.A. / Stoye, J.P. / Bishop, K.N. / Taylor, I.A.
CitationJournal: Nature / Year: 2014
Title: Structural Basis of Lentiviral Subversion of a Cellular Protein Degradation Pathway.
Authors: Schwefel, D. / Groom, H.C.T. / Boucherit, V.C. / Christodoulou, E. / Walker, P.A. / Stoye, J.P. / Bishop, K.N. / Taylor, I.A.
History
DepositionOct 19, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Jan 8, 2014Group: Database references
Revision 1.3Jan 24, 2018Group: Advisory / Source and taxonomy / Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4May 8, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_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_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_conn.ptnr2_label_seq_id / _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: PROTEIN VPRBP
B: PROTEIN VPX
C: DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1666
Polymers62,7133
Non-polymers4543
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-28.8 kcal/mol
Surface area19220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.250, 82.881, 115.561
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 3 types, 3 molecules ABC

#1: Protein PROTEIN VPRBP / DDB1- AND CUL4-ASSOCIATED FACTOR 1 / HIV-1 VPR-BINDING PROTE IN / VPRBP / VPR-INTERACTING PROTEIN / DCAF1


Mass: 41073.129 Da / Num. of mol.: 1 / Fragment: RESIDUES 1058-1396
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PTRIEX-6 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q9Y4B6
#2: Protein PROTEIN VPX / VIRAL PROTEIN X / X ORF PROTEIN / VPX


Mass: 13587.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SIMIAN IMMUNODEFICIENCY VIRUS / Strain: SOOTY MANGABEY / Variant: ISOLATE PBJ14/BCL-3 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): ROSETTA2 / References: UniProt: P19508
#3: 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 PR OTEIN 1 / SAMHD1


Mass: 8051.963 Da / Num. of mol.: 1 / Fragment: RESIDUES 582-626
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): ROSETTA2
References: UniProt: Q9Y3Z3, Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases

-
Non-polymers , 3 types, 28 molecules

#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.74 Å3/Da / Density % sol: 55.09 % / Description: NONE
Crystal growDetails: 0.2 M MAGNESIUM CHLORIDE, 0.1 M HEPES PH 7.5, 15% PEG 400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.46→30 Å / Num. obs: 25520 / % possible obs: 99.3 % / Observed criterion σ(I): 3.5 / Redundancy: 6.5 % / Biso Wilson estimate: 39.78 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.9
Reflection shellResolution: 2.56→2.61 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.6 / % possible all: 97.8

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.473→29.227 Å / SU ML: 0.29 / σ(F): 2 / Phase error: 21.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2164 1303 5.1 %
Rwork0.1757 --
obs0.1778 25518 97.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33 Å2
Refinement stepCycle: LAST / Resolution: 2.473→29.227 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3407 0 27 25 3459
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083516
X-RAY DIFFRACTIONf_angle_d1.1684750
X-RAY DIFFRACTIONf_dihedral_angle_d15.7631297
X-RAY DIFFRACTIONf_chiral_restr0.087507
X-RAY DIFFRACTIONf_plane_restr0.005615
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4733-2.57230.33571350.25692167X-RAY DIFFRACTION82
2.5723-2.68930.28211490.21892705X-RAY DIFFRACTION100
2.6893-2.8310.25021360.20112703X-RAY DIFFRACTION100
2.831-3.00820.2681270.20032746X-RAY DIFFRACTION100
3.0082-3.24020.23831630.19032713X-RAY DIFFRACTION100
3.2402-3.56570.19711470.16922754X-RAY DIFFRACTION100
3.5657-4.08050.19551570.15722724X-RAY DIFFRACTION100
4.0805-5.13640.17431310.13852804X-RAY DIFFRACTION99
5.1364-29.22910.21171580.18492899X-RAY DIFFRACTION100
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)
10.02460.02240.03110.19630.11410.2785-0.06290.01650.0530.0615-0.16640.00290.01350.0512-0.18080.02650.0836-0.03280.03180.0970.03545.7881-29.494716.1946
20.01560.0029-0.00120.0115-0.01660.02510.02340.03850.048-0.06830.0178-0.04790.02070.01090.06550.1585-0.00190.17120.04930.1280.002611.0541-43.87772.9153
30.02630.03510.0290.06760.05180.14530.00240.00880.0105-0.085-0.0607-0.0710.1045-0.0023-0.0390.16780.02260.02210.10940.01840.16975.9072-58.074814.4512
4-0.00050.00130.00210.0060.00420.0021-0.04280.01990.0188-0.0266-0.01310.02570.0093-0.0769-00.138-0.028-0.00660.1365-0.01140.1727-0.0594-45.491325.0809
50.0862-0.0038-0.01270.10280.0480.0537-0.01640.04910.02170.12640.01450.00220.0488-0.0080.00120.12410.03030.00890.12050.00210.0939-0.8615-36.050627.9843
60.026-0.00640.00450.00870.00070.00390.02080.03620.0296-0.01940.01160.0263-0.0172-0.02990.02090.0935-0.00870.00280.20580.09530.155611.8115-19.77168.7156
70.00230.0025-0.00080.0023-0.00650.00510.03270.03640.0073-0.02220.00370.00880.0015-0.01720.0274-0.0040.0594-0.05740.13740.08720.0528-9.8988-25.7399-1.8644
80.0081-0.0044-0.00250.0072-0.00130.0005-0.0048-0.02650.003-0.01360.0250.01550.0079-0.0280.01170.08380.0226-0.00390.21690.07040.1734-22.3817-28.11247.1356
90.00130.0015-0.00210.00350.00410.01840.001-0.0388-0.00360.0181-0.02980.02190.0102-0.0421-00.07160.0066-0.0070.0858-0.00020.0542-14.1855-24.81188.9621
100.0015-0.0034-0.00230.0030.00280.00290.00580.01780.0132-0.00430.0077-0.0110.00290.030600.4340.0306-0.03850.3304-0.0420.4421-5.9518-38.00381.5569
110.00370.00230.00190.00290.00180.0012-0.01510.0009-0.00740.0021-0.01310.0106-0.0057-0.0044-00.2127-0.03470.01660.13480.03550.239813.5757-16.16231.3131
120.0018-0.00130.00250.001-0.00140.00460.00170.00780.0048-0.00880.0141-0.0115-0.0020.00200.16530.02030.05620.23360.08360.3681.9331-10.3658-2.2059
130.0016-0.0009-0.00010.0016-0.00140.00240.0038-0.00420.0038-0.00170.0017-0.0014-0.0017-0.0125-00.3462-0.0037-0.03160.32580.06120.37752.3615-9.29685.4793
140.00710.0049-0.01210.0037-0.00850.02080.0106-0.00780.00630.01480.0007-0.0068-0.00010.00090.00890.1166-0.0031-0.04660.2342-0.02760.2322-7.8237-12.81146.3075
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1073 THROUGH 1169 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 1170 THROUGH 1214 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 1215 THROUGH 1290 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 1291 THROUGH 1332 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 1333 THROUGH 1392 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 5 THROUGH 17 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 18 THROUGH 38 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 39 THROUGH 56 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 57 THROUGH 84 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 85 THROUGH 103 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 104 THROUGH 111 )
12X-RAY DIFFRACTION12CHAIN C AND (RESID 606 THROUGH 610 )
13X-RAY DIFFRACTION13CHAIN 'C' AND (RESID 611 THROUGH 616 )
14X-RAY DIFFRACTION14CHAIN C AND (RESID 617 THROUGH 624 )

+
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