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- PDB-9wp1: Structural insights into tyrosine sulfation of CCR5 by human tyro... -

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Basic information

Entry
Database: PDB / ID: 9wp1
TitleStructural insights into tyrosine sulfation of CCR5 by human tyrosylprotein sulfotransferase-1
Components
  • C-C chemokine receptor type 5
  • Protein-tyrosine sulfotransferase 1
KeywordsTRANSFERASE / sulfotransferase / sulfation
Function / homology
Function and homology information


peptidyl-tyrosine sulfation / protein-tyrosine sulfotransferase / protein-tyrosine sulfotransferase activity / chemokine (C-C motif) ligand 5 binding / Defective F8 sulfation at Y1699 / Cytosolic sulfonation of small molecules / Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / negative regulation of macrophage apoptotic process / chemokine receptor activity ...peptidyl-tyrosine sulfation / protein-tyrosine sulfotransferase / protein-tyrosine sulfotransferase activity / chemokine (C-C motif) ligand 5 binding / Defective F8 sulfation at Y1699 / Cytosolic sulfonation of small molecules / Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / negative regulation of macrophage apoptotic process / chemokine receptor activity / signaling / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / C-C chemokine binding / response to cholesterol / C-C chemokine receptor activity / Chemokine receptors bind chemokines / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / dendritic cell chemotaxis / Interleukin-10 signaling / Binding and entry of HIV virion / cellular defense response / coreceptor activity / post-translational protein modification / calcium-mediated signaling / cell chemotaxis / trans-Golgi network / Golgi lumen / chemotaxis / calcium ion transport / MAPK cascade / cell-cell signaling / cellular response to lipopolysaccharide / positive regulation of cytosolic calcium ion concentration / virus receptor activity / actin binding / G alpha (i) signalling events / cell surface receptor signaling pathway / endosome / immune response / inflammatory response / G protein-coupled receptor signaling pathway / external side of plasma membrane / Golgi membrane / Golgi apparatus / cell surface / protein homodimerization activity / membrane / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Protein-tyrosine sulfotransferase / Sulfotransferase family / CC chemokine receptor 5 / Chemokine receptor family / : / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-3'-5'-DIPHOSPHATE / Protein-tyrosine sulfotransferase 1 / C-C chemokine receptor type 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsTanaka, S. / Asano, H. / Toyoda, K. / Nishiyori, T. / Kojo, H. / Nishimoto, E. / Teramoto, T. / Kakuta, Y.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP21K05384 Japan
Japan Society for the Promotion of Science (JSPS)24K09353 Japan
Japan Society for the Promotion of Science (JSPS)25H01276 Japan
CitationJournal: Febs J. / Year: 2026
Title: Structural insights into tyrosine sulfation of CCR5 by human tyrosylprotein sulfotransferase-1.
Authors: Tanaka, S. / Asano, H. / Toyoda, K. / Nishiyori, T. / Kojo, H. / Kiyomatsu, K. / Kurogi, K. / Sakakibara, Y. / Nishimoto, E. / Teramoto, T. / Kakuta, Y.
History
DepositionSep 8, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein-tyrosine sulfotransferase 1
B: Protein-tyrosine sulfotransferase 1
C: Protein-tyrosine sulfotransferase 1
D: Protein-tyrosine sulfotransferase 1
E: Protein-tyrosine sulfotransferase 1
F: Protein-tyrosine sulfotransferase 1
G: Protein-tyrosine sulfotransferase 1
H: Protein-tyrosine sulfotransferase 1
L: C-C chemokine receptor type 5
M: C-C chemokine receptor type 5
N: C-C chemokine receptor type 5
O: C-C chemokine receptor type 5
P: C-C chemokine receptor type 5
Q: C-C chemokine receptor type 5
R: C-C chemokine receptor type 5
S: C-C chemokine receptor type 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)260,74236
Polymers256,86916
Non-polymers3,87420
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Protein-tyrosine sulfotransferase 1
B: Protein-tyrosine sulfotransferase 1
L: C-C chemokine receptor type 5
M: C-C chemokine receptor type 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1869
Polymers64,2174
Non-polymers9685
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-58 kcal/mol
Surface area22670 Å2
MethodPISA
3
C: Protein-tyrosine sulfotransferase 1
D: Protein-tyrosine sulfotransferase 1
N: C-C chemokine receptor type 5
O: C-C chemokine receptor type 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1869
Polymers64,2174
Non-polymers9685
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7190 Å2
ΔGint-63 kcal/mol
Surface area22520 Å2
MethodPISA
4
E: Protein-tyrosine sulfotransferase 1
F: Protein-tyrosine sulfotransferase 1
P: C-C chemokine receptor type 5
Q: C-C chemokine receptor type 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1869
Polymers64,2174
Non-polymers9685
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-61 kcal/mol
Surface area22530 Å2
MethodPISA
5
G: Protein-tyrosine sulfotransferase 1
H: Protein-tyrosine sulfotransferase 1
R: C-C chemokine receptor type 5
S: C-C chemokine receptor type 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1869
Polymers64,2174
Non-polymers9685
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7320 Å2
ΔGint-63 kcal/mol
Surface area22470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.914, 189.398, 121.481
Angle α, β, γ (deg.)90.00, 125.98, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Protein-tyrosine sulfotransferase 1 / Tyrosylprotein sulfotransferase 1 / TPST-1


Mass: 31366.777 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TPST1 / Production host: Escherichia coli (E. coli)
References: UniProt: O60507, protein-tyrosine sulfotransferase
#2: Protein/peptide
C-C chemokine receptor type 5 / C-C CKR-5 / CC-CKR-5 / CCR-5 / CCR5 / CHEMR13 / HIV-1 fusion coreceptor


Mass: 741.810 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P51681
#3: Chemical
ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: 2.88 Å3/Da / Density % sol: 57.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9 / Details: 1.8 M sodium/potassium phosphate,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 56568 / % possible obs: 99.9 % / Redundancy: 3.7 % / CC1/2: 0.99 / Net I/σ(I): 2.73
Reflection shellResolution: 3.2→3.26 Å / Num. unique obs: 5656 / CC1/2: 0.484

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AP1

3ap1


Resolution: 3.2→49.21 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3225 2946 5.21 %
Rwork0.2728 --
obs0.2754 56568 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17914 0 228 0 18142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00418570
X-RAY DIFFRACTIONf_angle_d0.77125162
X-RAY DIFFRACTIONf_dihedral_angle_d4.9442457
X-RAY DIFFRACTIONf_chiral_restr0.052769
X-RAY DIFFRACTIONf_plane_restr0.0063143
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.250.37861180.32732246X-RAY DIFFRACTION87
3.25-3.310.40631570.31832539X-RAY DIFFRACTION99
3.31-3.370.3611500.3222547X-RAY DIFFRACTION100
3.37-3.430.37071470.29772546X-RAY DIFFRACTION99
3.43-3.50.36721510.29982548X-RAY DIFFRACTION100
3.5-3.580.35231360.29392551X-RAY DIFFRACTION100
3.58-3.660.35971360.28042564X-RAY DIFFRACTION100
3.66-3.750.37631490.27532572X-RAY DIFFRACTION100
3.75-3.850.28461460.26242558X-RAY DIFFRACTION100
3.85-3.970.31081410.25472554X-RAY DIFFRACTION100
3.97-4.090.26761170.25432592X-RAY DIFFRACTION100
4.09-4.240.33711510.26172567X-RAY DIFFRACTION100
4.24-4.410.29571340.24732590X-RAY DIFFRACTION100
4.41-4.610.31551510.24742585X-RAY DIFFRACTION100
4.61-4.850.2621370.24012532X-RAY DIFFRACTION100
4.85-5.160.28221370.2442597X-RAY DIFFRACTION100
5.16-5.550.31841450.27372585X-RAY DIFFRACTION100
5.55-6.110.35041500.29122579X-RAY DIFFRACTION100
6.11-6.990.31531330.28472576X-RAY DIFFRACTION100
7-8.80.27041320.25832596X-RAY DIFFRACTION100
8.81-49.210.29131280.28152598X-RAY DIFFRACTION98

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