PDB-3mqc: Crystal Structure of Ectodomain of BST-2/Tetherin/CD317 (P21)

ID or keywords:

Entry

Database: PDB / ID: 3mqc

Title

Crystal Structure of Ectodomain of BST-2/Tetherin/CD317 (P21)

Components

Bone marrow stromal antigen 2

Keywords

ANTIVIRAL PROTEIN / HIV

Function / homology

Function and homology information

negative regulation of plasmacytoid dendritic cell cytokine production / negative regulation of intracellular transport of viral material / response to interferon-beta / response to interferon-alpha / metalloendopeptidase inhibitor activity / positive regulation of leukocyte proliferation / azurophil granule membrane / negative regulation of viral genome replication / response to type II interferon / B cell activation ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Xiong, Y. / Yang, H. / Wang, J. / Meng, W.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural insight into the mechanisms of enveloped virus tethering by tetherin.
Authors: Yang, H. / Wang, J. / Jia, X. / McNatt, M.W. / Zang, T. / Pan, B. / Meng, W. / Wang, H.W. / Bieniasz, P.D. / Xiong, Y.

History

Deposition	Apr 27, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 27, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Sep 6, 2023	Group: 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 / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 1.3	Nov 22, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3mqc.cif.gz	90 KB	Display	PDBx/mmCIF format
PDB format	pdb3mqc.ent.gz	71 KB	Display	PDB format
PDBx/mmJSON format	3mqc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3mqc_validation.pdf.gz	456.6 KB	Display	wwPDB validaton report
Full document	3mqc_full_validation.pdf.gz	463.5 KB	Display
Data in XML	3mqc_validation.xml.gz	14.9 KB	Display
Data in CIF	3mqc_validation.cif.gz	20.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mq/3mqc ftp://data.pdbj.org/pub/pdb/validation_reports/mq/3mqc	HTTPS FTP

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Related structure data

Related structure data	3mq7SC 3mq9C 3mqbC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3nwh-d 4gkw-d 2efs-2 3mqb-3 2efs-1 4pxu-d 4pxt-d 6snz-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#163 - Jul 2013 HIV Capsid similarity (1)

Deposited unit

A: Bone marrow stromal antigen 2

B: Bone marrow stromal antigen 2

C: Bone marrow stromal antigen 2

D: Bone marrow stromal antigen 2

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

1

Idetical with deposited unit
defined by software

2

A: Bone marrow stromal antigen 2

C: Bone marrow stromal antigen 2

B: Bone marrow stromal antigen 2

D: Bone marrow stromal antigen 2

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

Unit cell

Length a, b, c (Å)	26.310, 58.980, 163.260
Angle α, β, γ (deg.)	90.00, 90.82, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	SER	SER	VAL	VAL	A	A	10 - 44	10 - 44
2	1	SER	SER	VAL	VAL	B	B	10 - 44	10 - 44
1	2	GLU	GLU	LEU	LEU	A	A	45 - 76	45 - 76
2	2	GLU	GLU	LEU	LEU	B	B	45 - 76	45 - 76
1	3	GLU	GLU	ALA	ALA	A	A	77 - 109	77 - 109
2	3	GLU	GLU	ALA	ALA	B	B	77 - 109	77 - 109
1	4	SER	SER	VAL	VAL	C	C	10 - 44	10 - 44
2	4	SER	SER	VAL	VAL	D	D	10 - 44	10 - 44
1	5	GLU	GLU	LEU	LEU	C	C	45 - 76	45 - 76
2	5	GLU	GLU	LEU	LEU	D	D	45 - 76	45 - 76
1	6	GLU	GLU	ALA	ALA	C	C	77 - 109	77 - 109
2	6	GLU	GLU	ALA	ALA	D	D	77 - 109	77 - 109
1	7	SER	SER	VAL	VAL	A	A	10 - 44	10 - 44
2	7	SER	SER	VAL	VAL	C	C	10 - 44	10 - 44
1	8	GLU	GLU	LEU	LEU	A	A	45 - 76	45 - 76
2	8	GLU	GLU	LEU	LEU	C	C	45 - 76	45 - 76
1	9	GLU	GLU	ALA	ALA	A	A	77 - 109	77 - 109
2	9	GLU	GLU	ALA	ALA	C	C	77 - 109	77 - 109
1	10	SER	SER	VAL	VAL	B	B	10 - 44	10 - 44
2	10	SER	SER	VAL	VAL	D	D	10 - 44	10 - 44
1	11	GLU	GLU	LEU	LEU	B	B	45 - 76	45 - 76
2	11	GLU	GLU	LEU	LEU	D	D	45 - 76	45 - 76
1	12	GLU	GLU	ALA	ALA	B	B	77 - 109	77 - 109
2	12	GLU	GLU	ALA	ALA	D	D	77 - 109	77 - 109

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12

#1: Protein	Bone marrow stromal antigen 2 / BST-2 / Tetherin / HM1.24 antigen Mass: 13647.592 Da / Num. of mol.: 4 / Fragment: residues 47-161 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BST2 / Plasmid: pMAT9s / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q10589
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.32 Å³/Da / Density % sol: 46.99 %
Crystal grow	Temperature: 298 K / Method: evaporation / pH: 7.5 Details: Crystals were grown at 25C using the microbatch under-oil method by mixing protein with crystallization buffer containing 100 mM HEPES, pH 7.5, 30% PEG 4000. 3-6% DMSO and 0.2-0.5 mM TCEP ...Details: Crystals were grown at 25C using the microbatch under-oil method by mixing protein with crystallization buffer containing 100 mM HEPES, pH 7.5, 30% PEG 4000. 3-6% DMSO and 0.2-0.5 mM TCEP were used as additives for optimal crystal growth. Micro batch under oil, pH 7.5, EVAPORATION, temperature 298.0K

Crystal

Density Matthews: 2.32 Å³/Da / Density % sol: 46.99 %

Crystal grow

Temperature: 298 K / Method: evaporation / pH: 7.5
Details: Crystals were grown at 25C using the microbatch under-oil method by mixing protein with crystallization buffer containing 100 mM HEPES, pH 7.5, 30% PEG 4000. 3-6% DMSO and 0.2-0.5 mM TCEP ...

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Data collection

Diffraction	Mean temperature: 110 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0723 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 16, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0723 Å / Relative weight: 1
Reflection	Resolution: 2.8→20 Å / Num. obs: 11940 / % possible obs: 95.4 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / R_merge(I) obs: 0.123 / R_sym value: 0.123 / Net I/σ(I): 9
Reflection shell	Resolution: 2.8→2.87 Å / R_merge(I) obs: 0.74 / Mean I/σ(I) obs: 2 / R_sym value: 0.74 / % possible all: 77.6

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
REFMAC	5.5.0102	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3MQ7

3mq7

Resolution: 2.8→19.63 Å / Cor.coef. F_o:F_c: 0.93 / Cor.coef. F_o:F_c free: 0.891 / SU B: 45.133 / SU ML: 0.399 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / ESU R Free: 0.438 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.29435	597	5 %	RANDOM
R_work	0.25848	-	-	-
obs	0.2603	11332	100 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 38.983 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.58 Å²	0 Å²	5.6 Å²
2-	-	8.27 Å²	0 Å²
3-	-	-	-4.52 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→19.63 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3096	0	0	3	3099

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.021	3110
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.417	1.956	4176
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.222	5	396
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.254	25.61	164
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	22.93	15	612
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.59	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	492
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	2304
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	3.947	6	1980
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	7.001	9	3152
X-RAY DIFFRACTION	r_scbond_it	9.103	9	1130
X-RAY DIFFRACTION	r_scangle_it	14.518	12	1024
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	275	TIGHT POSITIONAL	0.05	0.05
1	A	275	TIGHT THERMAL	3.21	4
2	A	235	TIGHT POSITIONAL	0.04	0.05
2	A	235	TIGHT THERMAL	1.67	4
3	A	264	TIGHT POSITIONAL	0.04	0.05
3	A	264	TIGHT THERMAL	1.7	4
4	C	275	TIGHT POSITIONAL	0.06	0.05
4	C	275	TIGHT THERMAL	3.28	4
5	C	235	TIGHT POSITIONAL	0.04	0.05
5	C	235	TIGHT THERMAL	2.48	4
6	C	264	TIGHT POSITIONAL	0.04	0.05
6	C	264	TIGHT THERMAL	1.96	4
7	A	275	TIGHT POSITIONAL	0.06	0.05
7	A	275	TIGHT THERMAL	3.18	4
8	A	235	TIGHT POSITIONAL	0.04	0.05
8	A	235	TIGHT THERMAL	2.14	4
9	A	264	TIGHT POSITIONAL	0.03	0.05
9	A	264	TIGHT THERMAL	1.99	4
10	B	275	TIGHT POSITIONAL	0.05	0.05
10	B	275	TIGHT THERMAL	3.32	4
11	B	235	TIGHT POSITIONAL	0.03	0.05
11	B	235	TIGHT THERMAL	2.26	4
12	B	264	TIGHT POSITIONAL	0.03	0.05
12	B	264	TIGHT THERMAL	2.23	4

LS refinement shell

Resolution: 2.8→2.871 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.393	34	-
R_work	0.313	643	-
obs	-	-	100 %

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	11.7719	0.9417	-10.0913	0.7727	-1.6609	8.9788	0.0874	-0.2913	-0.7395	-0.0065	-0.4053	0.1595	-0.3547	0.3681	0.3179	0.2082	0.0236	-0.0963	0.1813	-0.0142	0.2234	4.775	36.992	38.982
2	2.5287	1.8215	-6.8705	2.3741	-2.3197	13.8277	0.7201	0.2904	0.0536	0.2813	-0.5587	0.2631	-1.479	-0.4444	-0.1614	0.1705	0.0067	-0.0484	0.4787	-0.0007	0.0708	-26.011	39.062	78.137
3	19.6704	3.5999	-31.3278	0.5254	-5.4335	53.1435	-0.1353	-0.0347	-0.266	-0.2508	-0.0514	-0.2171	-0.6354	-0.2295	0.1867	0.3748	0.067	0.1306	0.0222	-0.0508	0.2651	-51.76	36.349	118.118
4	6.7253	3.646	-7.7758	2.9914	-4.2003	10.801	0.409	-0.1838	0.0198	0.3229	-0.3351	-0.1589	-0.85	0.3153	-0.074	0.2108	-0.0043	-0.1163	0.0575	-0.0287	0.2125	11.061	45.813	46.105
5	19.3161	5.7552	-17.4522	1.8906	-4.9374	15.1245	-0.4296	-0.4657	-0.9351	0.04	-0.2833	-0.2639	0.4428	0.4857	0.7129	0.2043	0.011	-0.0059	0.3793	0.0521	0.0949	-20.413	32.353	82.146
6	18.881	1.4906	-21.626	0.6455	-0.2102	28.0206	0.0477	0.6898	-0.3912	-0.2424	-0.3369	0.0805	-0.739	-0.9145	0.2891	0.233	-0.0577	0.0378	0.1803	-0.0685	0.1424	-55.031	29.548	114.906
7	5.3762	-0.761	-8.7259	0.7656	0.819	14.5917	0.3991	-0.0451	0.4734	-0.0841	-0.1816	0.0171	-0.7462	-0.0232	-0.2175	0.2286	-0.0076	-0.1255	0.0604	-0.056	0.2923	4.828	46.833	40.402
8	24.6644	1.7523	-21.2883	2.0228	-1.1411	19.351	-1.2709	0.6295	-1.3024	-0.3519	0.2133	-0.0894	1.034	-0.7182	1.0576	0.1785	-0.0292	-0.0326	0.1226	0.0168	0.117	36.144	43.573	1.817
9	10.1484	-1.0554	-14.2218	0.4714	1.7437	18.0906	-0.911	-0.1025	-2.0688	0.2818	-0.6953	-0.1764	0.6729	0.2063	1.6063	0.3865	0.0444	0.2652	0.3439	0.2655	0.5341	71.197	45.808	-30.653
10	4.5405	-1.8108	-3.6918	-0.0346	1.2397	2.7169	-0.3834	-0.161	-0.3598	0.0492	0.0301	0.0621	0.3511	0.1824	0.3533	0.1649	0.0211	-0.1212	0.0967	-0.0238	0.2574	11.231	36.098	44.204
11	3.924	0.54	-10.133	-0.1212	-1.5021	19.7201	0.8378	-1.167	-0.8974	0.2212	-1.132	-0.2775	-2.3074	1.4663	0.2942	0.2754	-0.024	0.0354	1.0347	0.2059	0.1661	41.97	49.016	7.139
12	6.6185	0.5133	-13.2225	-0.1027	0.0387	26.8765	-0.1913	-0.0772	-0.7333	-0.0783	-0.21	-0.1409	-0.039	0.0741	0.4013	0.3222	0.0289	0.0815	0.1342	0.093	0.2333	67.932	53.079	-32.496

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	11 - 44
2	X-RAY DIFFRACTION	2	A	45 - 76
3	X-RAY DIFFRACTION	3	A	77 - 109
4	X-RAY DIFFRACTION	4	B	11 - 44
5	X-RAY DIFFRACTION	5	B	45 - 76
6	X-RAY DIFFRACTION	6	B	77 - 109
7	X-RAY DIFFRACTION	7	C	11 - 44
8	X-RAY DIFFRACTION	8	C	45 - 76
9	X-RAY DIFFRACTION	9	C	77 - 109
10	X-RAY DIFFRACTION	10	D	11 - 44
11	X-RAY DIFFRACTION	11	D	45 - 76
12	X-RAY DIFFRACTION	12	D	77 - 109

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