PDB-9ulm: Mogamulizumab in complex with CCR4 N-terminus peptide (N2-C29)

ID or keywords:

Entry

Database: PDB / ID: 9ulm

Title

Mogamulizumab in complex with CCR4 N-terminus peptide (N2-C29)

Components

C-C chemokine receptor type 4
anti-kappa VHH
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 /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.01 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	9ulm.cif.gz	453.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9ulm.ent.gz	372.1 KB	Display	PDB format
PDBx/mmJSON format	9ulm.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/9ulm ftp://data.pdbj.org/pub/pdb/validation_reports/ul/9ulm	HTTPS FTP

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Related structure data

Related structure data	9ullC 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

K: anti-kappa VHH

I: anti-kappa VHH

X: C-C chemokine receptor type 4

Y: C-C chemokine receptor type 4

133 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: heavy chain

B: light chain

K: anti-kappa VHH

Y: C-C chemokine receptor type 4

defined by author
Evidence: gel filtration
66.5 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: heavy chain

D: light chain

I: anti-kappa VHH

X: C-C chemokine receptor type 4

defined by author
66.5 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	65.390, 71.190, 73.450
Angle α, β, γ (deg.)	81.24, 64.41, 71.05
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: Antibody	anti-kappa VHH Mass: 14365.709 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)
#4: Protein/peptide	C-C chemokine receptor type 4 / C-C CKR-4 / CC-CKR-4 / CCR-4 / CCR4 / K5-5 Mass: 3227.485 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P51679
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 874 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.19 Å³/Da / Density % sol: 43.89 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / Details: 0.1 M Sodium HEPES pH 6.5, 20% (W/V) PEG 10000

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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: Dec 30, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.01→50 Å / Num. obs: 70512 / % possible obs: 93.5 % / Redundancy: 1.8 % / CC_1/2: 0.995 / Net I/σ(I): 7.3
Reflection shell	Resolution: 2.01→2.07 Å / Num. unique obs: 3523 / CC_1/2: 0.792

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.01→29.55 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.32 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.244	3521	5 %
R_work	0.1965	-	-
obs	0.1989	70477	93.68 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.01→29.55 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8481	0	0	874	9355

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007
X-RAY DIFFRACTION	f_angle_d	0.885
X-RAY DIFFRACTION	f_dihedral_angle_d	6.329	1199
X-RAY DIFFRACTION	f_chiral_restr	0.054	1299
X-RAY DIFFRACTION	f_plane_restr	0.007	1512

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 (%)
2.01-2.04	0.3697	144	0.3079	2743	X-RAY DIFFRACTION	94
2.04-2.07	0.361	142	0.2995	2677	X-RAY DIFFRACTION	95
2.07-2.1	0.3269	145	0.2871	2753	X-RAY DIFFRACTION	95
2.1-2.13	0.3278	142	0.2686	2692	X-RAY DIFFRACTION	95
2.13-2.17	0.2826	142	0.2613	2715	X-RAY DIFFRACTION	95
2.17-2.2	0.2954	140	0.2432	2676	X-RAY DIFFRACTION	95
2.2-2.24	0.2715	144	0.2413	2743	X-RAY DIFFRACTION	95
2.24-2.29	0.3269	141	0.24	2686	X-RAY DIFFRACTION	94
2.29-2.33	0.2761	144	0.2351	2734	X-RAY DIFFRACTION	95
2.33-2.38	0.2971	141	0.2264	2666	X-RAY DIFFRACTION	94
2.38-2.44	0.2715	143	0.235	2715	X-RAY DIFFRACTION	94
2.44-2.5	0.3011	141	0.2195	2702	X-RAY DIFFRACTION	95
2.5-2.57	0.2877	142	0.2184	2692	X-RAY DIFFRACTION	95
2.57-2.64	0.2895	142	0.2122	2749	X-RAY DIFFRACTION	95
2.64-2.73	0.2805	142	0.2189	2693	X-RAY DIFFRACTION	94
2.73-2.82	0.2858	142	0.2136	2707	X-RAY DIFFRACTION	95
2.82-2.94	0.2487	142	0.2014	2695	X-RAY DIFFRACTION	94
2.94-3.07	0.2373	141	0.1979	2671	X-RAY DIFFRACTION	94
3.07-3.23	0.2188	140	0.1836	2655	X-RAY DIFFRACTION	93
3.23-3.44	0.2473	141	0.1831	2684	X-RAY DIFFRACTION	94
3.44-3.7	0.2094	141	0.1647	2690	X-RAY DIFFRACTION	94
3.7-4.07	0.1778	142	0.1631	2698	X-RAY DIFFRACTION	94
4.07-4.66	0.1742	137	0.1457	2595	X-RAY DIFFRACTION	91
4.66-5.86	0.2074	133	0.1531	2533	X-RAY DIFFRACTION	89
5.86-29.55	0.2357	127	0.1901	2392	X-RAY DIFFRACTION	84

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	3.0755	-1.3973	-1.0428	1.8377	0.5568	3.5422	0.0817	-0.0509	0.1223	0.0908	0.0077	-0.2772	0.0627	0.3608	-0.1064	0.2254	0.0162	-0.0477	0.2425	-0.01	0.195	40.7278	0.9278	65.1982
2	2.3523	-0.5005	0.0797	2.4349	-0.4471	3.2667	-0.03	0.2048	0.1593	-0.175	-0.0415	0.0943	0.0589	0.2684	0.0803	0.1407	-0.0253	0.0072	0.172	-0.0054	0.2392	39.4612	-0.33	32.5466
3	2.1737	0.0412	0.13	0.9282	-0.0496	4.2656	-0.0029	-0.183	-0.0338	0.0081	0.0265	0.1196	-0.2335	-0.4127	-0.0568	0.2369	0.0913	-0.0176	0.266	0.0124	0.2	18.2737	2.5559	63.1632
4	3.2275	0.858	-1.1911	0.7192	0.7033	4.0563	-0.0773	0.0327	0.4517	-0.1311	0.0971	-0.0165	-0.3082	-0.4863	-0.0444	0.2919	0.0673	-0.0404	0.3195	-0.0014	0.2656	19.3353	5.5469	55.1802
5	0.3684	0.1439	0.5625	0.4343	0.6893	2.3748	0.0295	-0.0031	-0.1636	-0.0025	0.1091	-0.1913	0.2117	0.294	-0.1047	0.2279	0.0189	-0.0156	0.2269	-0.0173	0.2798	26.7971	-8.8019	36.7948
6	3.5963	-1.4938	-0.65	3.9308	2.2776	3.7696	0.0704	0.0984	-0.2721	-0.2184	0.1679	-0.2482	0.1509	0.2697	-0.1691	0.2138	-0.0243	-0.0191	0.2383	0.0182	0.2063	26.694	-11.0226	28.2223
7	3.8388	-0.3325	0.7973	0.7322	-0.0815	1.6006	0.1235	-0.2353	-0.1619	0.2564	-0.007	0.0515	0.0512	-0.1695	-0.0804	0.4719	0.0716	-0.0689	0.2863	0.009	0.2381	59.0155	28.0795	45.1236
8	2.5991	-0.3406	1.0503	4.459	1.4596	2.7782	0.0037	-0.2348	-0.23	0.1843	0.099	0.5567	0.2461	-0.3503	-0.0709	0.2627	0.0146	0.0127	0.2329	0.0878	0.3292	34.9933	25.913	22.4813
9	2.3008	0.5488	0.1746	1.2299	-0.1563	2.8249	0.1944	0.3631	-0.2072	0.2306	0.0088	-0.1005	0.0703	0.5726	-0.1865	0.3871	0.0886	-0.1183	0.4209	-0.0912	0.2971	72.4599	25.8107	27.6262
10	2.9363	-0.1066	2.6345	0.8261	-0.1497	2.1854	0.1259	0.359	-0.2612	0.0963	0.108	-0.0045	0.1198	0.3252	-0.2194	0.3176	0.0443	-0.0324	0.3021	-0.0228	0.2085	59.7079	28.7544	21.515
11	3.3843	-0.1974	0.3383	1.8078	0.1896	4.8955	0.1671	0.2956	0.2841	-0.1258	-0.0509	0.2109	-0.3818	-0.0374	-0.1188	0.2748	0.0047	-0.0171	0.2057	0.0456	0.2077	41.5747	38.3439	11.8424
12	4.7544	-3.4831	1.0791	5.6564	-2.1929	2.8843	0.1973	-0.4848	-0.9053	-0.0695	0.0486	0.7328	0.4155	-0.3127	-0.2393	0.2026	-0.0771	-0.0188	0.3682	0.0529	0.384	-8.6786	-8.0697	32.5535
13	5.8833	0.9766	-0.7156	5.0153	0.7446	3.3392	0.8301	-0.3209	-1.6343	-0.7894	-0.0412	1.0294	0.9358	0.1444	-0.4842	0.5954	0.0455	-0.1987	0.8344	0.2438	0.7055	2.5828	-19.9972	43.3581
14	5.1507	-1.6195	2.734	2.5306	0.597	8.0968	0.4304	0.3378	-0.1911	-0.2182	0.0353	-0.1477	0.4542	0.8345	-0.3141	0.2238	0.0426	-0.0626	0.2354	-0.0592	0.2574	2.8603	-6.476	28.5572
15	4.7217	-2.7889	2.9614	5.5755	-3.0501	5.2338	-0.2084	-0.6944	-0.078	0.8308	0.1443	0.2618	-0.0414	0.1972	-0.1517	0.3244	0.0313	-0.0055	0.3854	-0.0142	0.2087	6.8771	-5.836	44.0066
16	4.9608	-0.1287	0.1314	1.2012	0.2982	4.0683	-0.0421	-0.8322	-0.3146	0.1923	-0.1067	0.0747	0.1027	-0.0268	0.0747	0.167	-0.0108	0.0228	0.3145	0.0501	0.3253	-2.2987	-4.3373	38.9861
17	6.0582	-1.8112	1.4561	3.2188	-0.4084	1.701	0.1241	0.0094	-0.501	-0.0806	0.0623	0.3865	0.0674	0.0188	-0.2125	0.1925	0.0187	0.0369	0.1981	-0.0035	0.1646	2.4697	-6.8456	32.4272
18	7.3515	-5.3848	2.922	6.5024	-1.3299	4.6964	0.3668	0.3809	-0.6945	-0.2434	-0.2391	0.5753	0.2535	-0.1085	-0.2152	0.1875	-0.0862	-0.0108	0.3425	0.0148	0.2587	-2.9209	-9.9107	27.3336
19	2.9612	0.6636	0.4801	3.4237	-1.4723	3.6564	0.337	0.7481	0.7816	-0.5528	-0.7123	-0.4819	-0.0561	1.3578	0.036	0.5551	-0.0893	-0.0067	1.6471	0.2176	0.5236	64.9068	40.5456	-11.5283
20	0.1729	-0.3499	0.5556	1.4932	-0.6412	2.3435	0.1741	0.591	0.396	-0.5205	-0.6783	-0.8078	-0.5399	1.7403	-0.2378	0.4413	-0.2071	0.0557	1.7906	0.1533	0.3935	63.857	38.7542	-5.3698
21	5.0103	1.294	4.3744	6.3503	3.1207	4.555	-0.25	-0.2425	-0.039	-0.4389	-0.3455	0.8441	-0.0513	0.8552	0.4655	0.5558	0.0614	-0.1639	0.8036	-0.0855	0.3826	48.6323	31.2241	-13.529
22	5.8312	1.2519	3.4676	1.6259	1.7354	5.472	-0.238	0.0856	0.1477	-0.107	-0.5957	0.2474	-0.0807	-0.057	0.1404	0.575	0.1681	0.1559	1.3273	0.0262	0.2386	56.9722	33.0654	-4.0058
23	3.3985	0.2634	1.954	1.309	0.0693	2.2715	0.2601	0.852	-0.3296	-0.1957	-0.4172	-0.2788	0.3664	0.7797	-0.2731	0.3437	0.1712	-0.0323	1.4764	0.0763	0.4227	63.2099	29.353	1.9052
24	1.209	-1.1534	0.0007	1.2086	0.4258	2.0361	0.371	0.593	0.0009	-0.4814	-0.573	-0.9187	-0.1095	1.4135	-0.0749	0.4623	0.142	0.2572	2.271	0.1152	0.3198	68.6706	33.611	-6.315
25	0.6777	-0.0757	-1.0991	0.0078	0.1354	1.815	0.3538	0.2415	0.4508	-0.0962	0.06	-0.2854	-0.1876	0.3837	0.1741	0.1891	-0.261	0.2077	1.6829	0.2093	0.1756	58.754	38.1449	-7.9452
26	0.307	0.0991	-0.7426	0.3128	-0.5909	3.0145	0.6664	0.7471	0.1822	-0.0829	-0.1085	0.3659	-0.5437	0.9253	-0.092	0.5658	-0.1115	-0.2178	1.3337	0.008	0.2829	58.0626	40.3927	-2.7856
27	2.1592	0.457	-2.5061	4.3045	-1.8388	3.5515	0.2402	-0.2364	-0.1951	0.3452	0.178	-0.0939	-0.5684	0.425	-0.4383	0.5974	0.0474	-0.2486	0.574	-0.0069	0.3975	77.5493	27.4943	47.4925
28	3.2914	1.605	-0.9835	5.4193	-0.7562	0.4772	0.2937	-0.5886	-0.3133	0.2906	-0.1998	-0.1047	0.0809	-0.1703	-0.1001	0.3748	0.0914	-0.0294	0.5596	0.0183	0.2716	31.577	1.489	79.3797

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 112 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 113 through 219 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 1 through 80 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 81 through 95 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 96 through 168 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 169 through 216 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 1 through 125 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 126 through 219 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 1 through 66 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 67 through 133 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 134 through 217 )
12	X-RAY DIFFRACTION	12	chain 'K' and (resid 2 through 25 )
13	X-RAY DIFFRACTION	13	chain 'K' and (resid 26 through 32 )
14	X-RAY DIFFRACTION	14	chain 'K' and (resid 33 through 51 )
15	X-RAY DIFFRACTION	15	chain 'K' and (resid 52 through 60 )
16	X-RAY DIFFRACTION	16	chain 'K' and (resid 61 through 83 )
17	X-RAY DIFFRACTION	17	chain 'K' and (resid 84 through 107 )
18	X-RAY DIFFRACTION	18	chain 'K' and (resid 108 through 121 )
19	X-RAY DIFFRACTION	19	chain 'I' and (resid 2 through 17 )
20	X-RAY DIFFRACTION	20	chain 'I' and (resid 18 through 39 )
21	X-RAY DIFFRACTION	21	chain 'I' and (resid 40 through 44 )
22	X-RAY DIFFRACTION	22	chain 'I' and (resid 45 through 51 )
23	X-RAY DIFFRACTION	23	chain 'I' and (resid 52 through 67 )
24	X-RAY DIFFRACTION	24	chain 'I' and (resid 68 through 91 )
25	X-RAY DIFFRACTION	25	chain 'I' and (resid 92 through 99 )
26	X-RAY DIFFRACTION	26	chain 'I' and (resid 100 through 119 )
27	X-RAY DIFFRACTION	27	chain 'X' and (resid 14 through 24 )
28	X-RAY DIFFRACTION	28	chain 'Y' and (resid 14 through 24 )

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