PDB-9ull: Mogamulizumab in complex with CCR4 N-terminus peptide (S14-S24)

ID or keywords:

Entry

Database: PDB / ID: 9ull

Title

Mogamulizumab in complex with CCR4 N-terminus peptide (S14-S24)

Components

C-C chemokine receptor type 4
heavy chain
light chain

Keywords

IMMUNE SYSTEM / mogamulizumab / CCR4 / antibody

Function / homology

Function and homology information

chemokine receptor activity / C-C chemokine binding / C-C chemokine receptor activity / Chemokine receptors bind chemokines / calcium-mediated signaling / cell chemotaxis / chemotaxis / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / immune response ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SOLUTION SCATTERING /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.63 Å

Authors

Heo, Y.-S.

Funding support

1items

Citation

Journal: To Be Published
Title: Structural insights into the therapeutic efficacy and resistance of mogamulizumab
Authors: Heo, Y.-S.

History

Deposition	Apr 20, 2025	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 22, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9ull.cif.gz	372.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9ull.ent.gz	302.6 KB	Display	PDB format
PDBx/mmJSON format	9ull.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ul/9ull ftp://data.pdbj.org/pub/pdb/validation_reports/ul/9ull	HTTPS FTP

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Related structure data

Related structure data	9ulmC 9ulnC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #147 - Mar 2012 Rhodopsin similarity (6) #217 - Jan 2018 Opioid Receptors similarity (6) #100 - Apr 2008 Adrenergic Receptors similarity (6) #164 - Aug 2013 Serotonin Receptor similarity (6) #202 - Oct 2016 Dipeptidyl Peptidase 4 similarity (1) #136 - Apr 2011 Nanobodies similarity (6) #27 - Mar 2002 Bacteriorhodopsin similarity (6) #58 - Oct 2004 G Proteins similarity (6) #66 - Jun 2005 Carotenoid Oxygenase similarity (6)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#21 - Sep 2001
Antibodies
similarity (1)
#256 - Apr 2021
SARS-CoV-2 Spike and Antibodies
similarity (1)
#147 - Mar 2012
Rhodopsin
similarity (6)
#217 - Jan 2018
Opioid Receptors
similarity (6)
#100 - Apr 2008
Adrenergic Receptors
similarity (6)
#164 - Aug 2013
Serotonin Receptor
similarity (6)
#202 - Oct 2016
Dipeptidyl Peptidase 4
similarity (1)
#136 - Apr 2011
Nanobodies
similarity (6)
#27 - Mar 2002
Bacteriorhodopsin
similarity (6)
#58 - Oct 2004
G Proteins
similarity (6)
#66 - Jun 2005
Carotenoid Oxygenase
similarity (6)

Deposited unit

A: heavy chain

B: light chain

C: heavy chain

D: light chain

J: C-C chemokine receptor type 4

K: C-C chemokine receptor type 4

101 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: heavy chain

B: light chain

K: C-C chemokine receptor type 4

defined by author&software
Evidence: gel filtration
50.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: heavy chain

D: light chain

J: C-C chemokine receptor type 4

defined by author&software
50.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	41.270, 67.440, 87.830
Angle α, β, γ (deg.)	87.20, 82.70, 79.25
Int Tables number	1
Space group name H-M	P1

#1: Antibody	heavy chain Mass: 24809.686 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody	light chain Mass: 24117.945 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein/peptide	C-C chemokine receptor type 4 / C-C CKR-4 / CC-CKR-4 / CCR-4 / CCR4 / K5-5 Mass: 1401.476 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P51679
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1187 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment

Method	Number of used crystals
X-RAY DIFFRACTION	1
SOLUTION SCATTERING

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Sample preparation

Crystal	Density Matthews: 2.37 Å³/Da / Density % sol: 48.01 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Sodium HEPES pH 7.5, 20% (W/V) PEG 4000, 10% v/v 2-Propanol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 29, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.63→50 Å / Num. obs: 109257 / % possible obs: 94.8 % / Redundancy: 2 % / CC_1/2: 0.999 / Net I/σ(I): 11.3
Reflection shell	Resolution: 1.63→1.69 Å / Num. unique obs: 5298 / CC_1/2: 0.71

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Processing

Software

Name	Version	Classification
PHENIX	(1.20_4459: ???)	refinement
XDS		data scaling
XDS		data reduction
MOLREP		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.63→29.19 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 22.28 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1965	5462	5 %
R_work	0.1681	-	-
obs	0.1695	109223	94.83 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.63→29.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6776	0	0	1187	7963

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005
X-RAY DIFFRACTION	f_angle_d	0.765
X-RAY DIFFRACTION	f_dihedral_angle_d	6.252	955
X-RAY DIFFRACTION	f_chiral_restr	0.048	1051
X-RAY DIFFRACTION	f_plane_restr	0.005	1209

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.63-1.65	0.3587	183	0.3125	3478	X-RAY DIFFRACTION	93
1.65-1.67	0.303	175	0.2899	3354	X-RAY DIFFRACTION	93
1.67-1.69	0.2785	181	0.2656	3426	X-RAY DIFFRACTION	94
1.69-1.71	0.2846	182	0.2467	3463	X-RAY DIFFRACTION	94
1.71-1.73	0.2571	179	0.2476	3402	X-RAY DIFFRACTION	94
1.73-1.76	0.2665	181	0.2324	3432	X-RAY DIFFRACTION	95
1.76-1.78	0.2531	182	0.2289	3457	X-RAY DIFFRACTION	94
1.78-1.81	0.2724	180	0.2278	3424	X-RAY DIFFRACTION	95
1.81-1.84	0.2261	179	0.2128	3394	X-RAY DIFFRACTION	94
1.84-1.87	0.25	185	0.1999	3503	X-RAY DIFFRACTION	94
1.87-1.9	0.2505	180	0.1995	3428	X-RAY DIFFRACTION	94
1.9-1.93	0.2472	178	0.1903	3381	X-RAY DIFFRACTION	93
1.93-1.97	0.2019	183	0.1761	3478	X-RAY DIFFRACTION	94
1.97-2.01	0.2169	178	0.1725	3388	X-RAY DIFFRACTION	95
2.01-2.05	0.2188	186	0.1767	3519	X-RAY DIFFRACTION	95
2.05-2.1	0.2018	178	0.1728	3387	X-RAY DIFFRACTION	94
2.1-2.15	0.2199	184	0.1685	3501	X-RAY DIFFRACTION	95
2.15-2.21	0.2166	182	0.1655	3454	X-RAY DIFFRACTION	95
2.21-2.28	0.2002	183	0.1645	3463	X-RAY DIFFRACTION	95
2.28-2.35	0.2178	182	0.1661	3466	X-RAY DIFFRACTION	96
2.35-2.43	0.2234	188	0.1688	3560	X-RAY DIFFRACTION	96
2.43-2.53	0.2084	180	0.1744	3438	X-RAY DIFFRACTION	96
2.53-2.65	0.1854	185	0.1665	3512	X-RAY DIFFRACTION	96
2.65-2.79	0.1863	185	0.1706	3499	X-RAY DIFFRACTION	96
2.79-2.96	0.1777	186	0.1594	3535	X-RAY DIFFRACTION	96
2.96-3.19	0.1789	183	0.1605	3482	X-RAY DIFFRACTION	95
3.19-3.51	0.1601	184	0.148	3490	X-RAY DIFFRACTION	96
3.51-4.02	0.1772	183	0.1407	3488	X-RAY DIFFRACTION	95
4.02-5.06	0.1476	184	0.1285	3489	X-RAY DIFFRACTION	96
5.06-29.19	0.1816	183	0.1644	3470	X-RAY DIFFRACTION	95

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	6.377	-3.2524	-5.7716	2.9671	3.6655	6.0265	-0.1795	-0.2502	-0.1088	0.1064	0.2244	-0.0278	0.1749	0.2349	-0.0565	0.1818	-0.0353	0.0144	0.1229	0.002	0.1383	46.3268	41.1002	40.1989
2	6.0177	-4.0407	-4.6678	4.8368	3.7079	5.0073	0.0462	-0.0955	-0.047	-0.0133	-0.0131	0.0283	0.0269	0.0903	-0.0543	0.1455	-0.0196	-0.0224	0.142	0.0108	0.0932	46.253	45.6604	41.2312
3	3.1683	-0.908	-2.3431	3.4606	1.4595	4.7262	-0.2013	0.0597	-0.2776	-0.2092	0.0426	-0.0387	0.6989	0.2167	0.1587	0.2652	0.037	0.0071	0.166	-0.0076	0.1591	49.1099	34.4017	34.0265
4	4.0139	-3.5347	0.7918	3.3888	-1.341	1.6447	0.1691	0.1175	0.6953	-0.056	-0.219	0.0986	-0.3149	0.0412	-0.0015	0.2716	-0.0096	0.0256	0.1491	-0.0293	0.3438	45.8595	91.7345	50.0568
5	6.8217	-1.5168	-1.3896	4.3543	0.7543	6.3359	-0.1295	-0.1619	-0.5386	-0.5197	-0.0443	0.3514	0.4904	-0.1858	0.1218	0.3243	-0.0599	-0.021	0.154	0.0352	0.2884	13.1414	22.5487	68.0765
6	1.9068	0.3022	1.2767	2.2295	0.5048	2.7736	0.0175	-0.1351	-0.0268	0.2083	0.0387	0.1827	-0.0481	-0.128	-0.0489	0.1859	-0.0087	0.0355	0.1324	0.0237	0.1546	15.2555	32.9223	81.0391
7	2.2597	-1.0004	0.6187	2.4782	1.5708	1.8309	-0.0725	-0.0063	0.2802	0.2834	0.0405	-0.3119	0.0071	-0.0367	0.0718	0.2229	-0.0368	0.0561	0.2037	0.0186	0.117	21.1014	60.2621	92.4011
8	2.1691	-2.3269	0.6405	3.7611	-0.8677	1.6516	0.0037	-0.0534	-0.0084	0.1113	0.0542	0.1911	0.2276	-0.113	-0.0501	0.2197	-0.0617	0.0159	0.1838	-0.0092	0.1463	15.374	62.6985	90.9917
9	0.277	0.1482	0.1	1.1269	0.1093	0.5172	0.0178	0.0027	-0.0532	-0.157	-0.0226	0.0354	0.0401	-0.0134	0.0056	0.1806	-0.0028	0.0182	0.1616	-0.0014	0.1835	20.186	47.3795	65.7921
10	2.9599	1.6437	3.0257	2.0587	2.1566	6.1483	0.0825	-0	-0.0432	0.1038	0.015	-0.1141	0.0986	0.1697	-0.0893	0.1493	0.0153	0.0353	0.1407	-0.0059	0.1449	29.7245	71.5643	82.9308
11	6.2267	-4.0026	-2.6816	4.0249	2.5278	3.111	0.1813	0.5489	0.2856	-0.5839	-0.1224	-0.0354	-0.2975	-0.239	-0.0408	0.3081	-0.0282	0.004	0.1829	0.0629	0.1647	44.457	80.0011	32.5492
12	3.7779	-0.0179	-0.2395	1.8984	0.5315	3.0601	-0.1599	0.188	0.0753	-0.2109	0.1426	-0.0616	-0.0164	0.0933	0.0068	0.2332	-0.033	0.0351	0.1335	0.01	0.155	51.1202	82.8843	39.9344
13	1.1702	-1.0146	-1.069	1.6999	1.3923	2.1643	-0.0241	0.1199	0.1215	-0.2622	0.0332	-0.0488	-0.0474	0.0316	-0.0123	0.276	-0.0307	0.0237	0.1856	0.0309	0.2096	49.2253	75.4964	36.1179
14	5.7652	1.9247	-0.9343	3.2357	-0.6518	4.0234	-0.0079	0.1253	-0.1059	-0.2484	0.1298	0.1619	0.0101	-0.3416	-0.1176	0.2108	0.0321	0.0078	0.1749	0.0098	0.1246	40.8161	51.4504	26.6345
15	1.6517	0.8986	0.1252	3.4985	-0.0815	1.071	-0.0126	-0.0485	0.0478	0.0302	-0.054	-0.0411	-0.0126	0.0327	0.0647	0.1407	0.012	0.0288	0.1393	-0.0166	0.15	44.9591	71.2711	56.6398
16	2.9959	1.5196	0.6181	3.6848	0.2532	1.2997	0.0422	-0.245	0.1987	0.2302	-0.047	0.3377	-0.11	-0.1355	0.017	0.2012	0.0102	0.0513	0.1835	-0.0255	0.192	37.3938	73.5531	59.8715
17	0.3426	-0.028	0.0786	1.1683	0.2182	0.3177	0.0016	0.0292	0.0007	-0.0314	-0.0038	0.0275	0.0348	-0.0367	0.0019	0.1667	-0.0148	0.005	0.1435	0.0071	0.1253	43.3835	57.4418	45.3015

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'D' and (resid 134 through 155 )
2	X-RAY DIFFRACTION	2	chain 'D' and (resid 156 through 179 )
3	X-RAY DIFFRACTION	3	chain 'D' and (resid 180 through 217 )
4	X-RAY DIFFRACTION	4	chain 'J' and (resid 15 through 24 )
5	X-RAY DIFFRACTION	5	chain 'K' and (resid 15 through 24 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 1 through 112 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 113 through 151 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 152 through 220 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1 through 133 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 134 through 217 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 1 through 33 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 34 through 76 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 77 through 125 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 126 through 219 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 1 through 53 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 54 through 80 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 81 through 133 )

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