PDB-3mqb: Crystal Structure of Ectodomain of BST-2/Tetherin/CD317 (C2)

ID or keywords:

Entry

Database: PDB / ID: 3mqb

Title

Crystal Structure of Ectodomain of BST-2/Tetherin/CD317 (C2)

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 / B cell activation / response to type II interferon ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.2 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 / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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 27, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3mqb.cif.gz	179.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3mqb.ent.gz	146.5 KB	Display	PDB format
PDBx/mmJSON format	3mqb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3mqb_validation.pdf.gz	456.3 KB	Display	wwPDB validaton report
Full document	3mqb_full_validation.pdf.gz	462.7 KB	Display
Data in XML	3mqb_validation.xml.gz	15.7 KB	Display
Data in CIF	3mqb_validation.cif.gz	21.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mq/3mqb ftp://data.pdbj.org/pub/pdb/validation_reports/mq/3mqb	HTTPS FTP

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Related structure data

Related structure data	3mq7SC 3mq9C 3mqcC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5to6-d 4xa6-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

E: Bone marrow stromal antigen 2

F: Bone marrow stromal antigen 2

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

1

A: Bone marrow stromal antigen 2

B: Bone marrow stromal antigen 2

E: Bone marrow stromal antigen 2

F: Bone marrow stromal antigen 2

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

2

A: Bone marrow stromal antigen 2

B: Bone marrow stromal antigen 2

A: Bone marrow stromal antigen 2

B: Bone marrow stromal antigen 2

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

3

E: Bone marrow stromal antigen 2

F: Bone marrow stromal antigen 2

E: Bone marrow stromal antigen 2

F: Bone marrow stromal antigen 2

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

Unit cell

Length a, b, c (Å)	181.650, 28.590, 94.510
Angle α, β, γ (deg.)	90.00, 111.43, 90.00
Int Tables number	5
Space group name H-M	C121

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	THR	THR	A	A	50 - 94	10 - 54
2	1	SER	SER	THR	THR	B	B	50 - 94	10 - 54
1	2	SER	SER	THR	THR	E	C	50 - 94	10 - 54
2	2	SER	SER	THR	THR	F	D	50 - 94	10 - 54
1	3	VAL	VAL	LEU	LEU	A	A	95 - 116	55 - 76
2	3	VAL	VAL	LEU	LEU	B	B	95 - 116	55 - 76
1	4	VAL	VAL	LEU	LEU	E	C	95 - 116	55 - 76
2	4	VAL	VAL	LEU	LEU	F	D	95 - 116	55 - 76
1	5	GLU	GLU	ALA	ALA	A	A	117 - 149	77 - 109
2	5	GLU	GLU	ALA	ALA	B	B	117 - 149	77 - 109
1	6	GLU	GLU	ALA	ALA	E	C	117 - 149	77 - 109
2	6	GLU	GLU	ALA	ALA	F	D	117 - 149	77 - 109
1	7	SER	SER	THR	THR	A	A	50 - 94	10 - 54
2	7	SER	SER	THR	THR	E	C	50 - 94	10 - 54
1	8	VAL	VAL	LEU	LEU	A	A	95 - 116	55 - 76
2	8	VAL	VAL	LEU	LEU	E	C	95 - 116	55 - 76
1	9	GLU	GLU	ALA	ALA	A	A	117 - 149	77 - 109
2	9	GLU	GLU	ALA	ALA	E	C	117 - 149	77 - 109
1	10	SER	SER	THR	THR	E	C	50 - 94	10 - 54
2	10	SER	SER	THR	THR	F	D	50 - 94	10 - 54
1	11	VAL	VAL	LEU	LEU	E	C	95 - 116	55 - 76
2	11	VAL	VAL	LEU	LEU	F	D	95 - 116	55 - 76
1	12	GLU	GLU	ALA	ALA	E	C	117 - 149	77 - 109
2	12	GLU	GLU	ALA	ALA	F	D	117 - 149	77 - 109

NCS ensembles :

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

Details

1

#1: Protein	Bone marrow stromal antigen 2 / BST-2 / Tetherin / HM1.24 antigen Mass: 13460.012 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
Has protein modification	Y

#1: Protein

Bone marrow stromal antigen 2 / BST-2 / Tetherin / HM1.24 antigen

Mass: 13460.012 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

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: 2.12 Å³/Da / Density % sol: 42.02 %
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., EVAPORATION, temperature 298.0K

Crystal

Density Matthews: 2.12 Å³/Da / Density % sol: 42.02 %

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: 1.0717 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0717 Å / Relative weight: 1
Reflection	Resolution: 3.2→30 Å / Num. obs: 7240 / % possible obs: 93.8 % / Observed criterion σ(I): -3 / Redundancy: 3 % / R_merge(I) obs: 0.081 / R_sym value: 0.081 / Net I/σ(I): 12.5
Reflection shell	Resolution: 3.2→3.31 Å / R_merge(I) obs: 0.569 / Mean I/σ(I) obs: 1.9 / R_sym value: 0.123 / % possible all: 96.7

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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: 3.2→20 Å / Cor.coef. F_o:F_c: 0.921 / Cor.coef. F_o:F_c free: 0.878 / SU B: 71.229 / SU ML: 0.571 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.766 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.31526	338	4.9 %	RANDOM
R_work	0.25534	-	-	-
obs	0.25832	6505	87.04 %	-

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: 59.349 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.41 Å²	-0 Å²	-2.23 Å²
2-	-	6.66 Å²	0 Å²
3-	-	-	-3.88 Å²

Refinement step

Cycle: LAST / Resolution: 3.2→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3305	0	0	0	3305

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.021	3328
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	2257
X-RAY DIFFRACTION	r_angle_refined_deg	1.111	1.96	4469
X-RAY DIFFRACTION	r_angle_other_deg	4.219	3	5532
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.625	5	419
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.239	25.543	175
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	22	15	654
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.492	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.062	0.2	515
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	3724
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	596
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	2.705	3	2098
X-RAY DIFFRACTION	r_mcbond_other	0	3	855
X-RAY DIFFRACTION	r_mcangle_it	5.542	4	3345
X-RAY DIFFRACTION	r_scbond_it	8.711	6	1230
X-RAY DIFFRACTION	r_scangle_it	15.386	9	1124
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	572	TIGHT POSITIONAL	0.5	0.05
1	A	572	TIGHT THERMAL	3.54	0.5
2	E	572	TIGHT POSITIONAL	0.63	0.05
2	E	572	TIGHT THERMAL	4.78	0.5
3	A	276	TIGHT POSITIONAL	0.2	0.05
3	A	276	TIGHT THERMAL	2.94	0.5
4	E	276	TIGHT POSITIONAL	0.12	0.05
4	E	276	TIGHT THERMAL	3.09	0.5
5	A	448	TIGHT POSITIONAL	0.52	0.05
5	A	448	TIGHT THERMAL	4.23	0.5
6	E	448	TIGHT POSITIONAL	0.48	0.05
6	E	448	TIGHT THERMAL	3.96	0.5
7	A	572	TIGHT POSITIONAL	0.56	0.05
7	A	572	TIGHT THERMAL	4.93	0.5
8	A	276	TIGHT POSITIONAL	0.37	0.05
8	A	276	TIGHT THERMAL	3	0.5
9	A	448	TIGHT POSITIONAL	0.55	0.05
9	A	448	TIGHT THERMAL	5.68	0.5
10	E	572	TIGHT POSITIONAL	0.63	0.05
10	E	572	TIGHT THERMAL	4.78	0.5
11	E	276	TIGHT POSITIONAL	0.12	0.05
11	E	276	TIGHT THERMAL	3.09	0.5
12	E	448	TIGHT POSITIONAL	0.48	0.05
12	E	448	TIGHT THERMAL	3.96	0.5

LS refinement shell

Resolution: 3.2→3.281 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.268	17	-
R_work	0.314	341	-
obs	-	-	65.33 %

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	14.1187	-2.3682	8.2839	4.6538	-1.2707	15.1931	-0.842	-1.1762	1.1164	-0.1887	0.4375	-0.3359	-0.9293	0.0103	0.4045	0.4906	0.1509	0.1967	0.6519	-0.1586	0.6857	81.9382	17.9434	53.2364
2	19.8423	1.2647	8.455	5.6086	3.0549	12.3562	-0.4803	0.8476	1.1436	-0.4349	-0.0639	0.8803	-0.9921	0.9832	0.5442	0.4319	-0.1029	-0.0095	0.6151	0.1388	0.521	64.2509	18.3071	33.866
3	20.4412	-0.172	13.182	2.8065	-2.5471	10.6183	0.1283	1.709	0.1833	0.4148	-0.4731	-0.288	-0.292	1.5119	0.3448	0.5227	0.0935	-0.023	1.0027	-0.0135	0.4688	43.8662	19.3039	10.7886
4	12.8285	-0.7049	14.6116	0.4442	-1.0644	16.9577	-0.0319	0.863	0.36	0.0345	-0.2197	-0.0875	-0.0676	1.1834	0.2516	0.3135	0.0856	0.2219	0.5424	-0.0545	0.4539	8.303	22.5339	-27.8317
5	3.5118	-1.7349	6.0346	3.0836	1.6069	20.3247	-0.1982	-0.1301	0.0445	0.0612	0.2798	-0.1189	0.027	0.1407	-0.0817	0.3728	-0.0595	0.1699	0.0693	0.0767	0.5505	62.0937	7.3888	99.2941
6	2.7088	0.4883	1.0751	1.2308	-3.4115	11.859	0.1146	-0.2943	-0.0524	-0.0614	0.0148	0.035	0.2009	-0.4811	-0.1294	0.4036	0.1528	0.1245	0.3729	-0.0776	0.4162	50.0822	7.4008	75.8116
7	5.5763	1.1941	9.745	0.7964	2.25	27.6685	0.1752	-0.3068	0.2102	0.0301	-0.0019	0.28	0.9231	-1.5679	-0.1733	0.35	0.062	0.0108	0.3563	0.0867	0.4904	37.9449	7.8716	47.4828
8	6.6931	-0.8871	13.0183	0.6545	-2.5946	26.9674	0.4353	-0.0315	-0.3	-0.2064	-0.3187	-0.0481	1.0974	0.1951	-0.1166	0.5133	0.2855	0.0028	0.6183	-0.2363	0.55	18.9439	8.8663	1.3229

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	50 - 68
2	X-RAY DIFFRACTION	1	B	50 - 68
3	X-RAY DIFFRACTION	2	A	69 - 86
4	X-RAY DIFFRACTION	2	B	69 - 86
5	X-RAY DIFFRACTION	3	A	87 - 109
6	X-RAY DIFFRACTION	3	B	87 - 109
7	X-RAY DIFFRACTION	4	A	110 - 158
8	X-RAY DIFFRACTION	4	B	110 - 158
9	X-RAY DIFFRACTION	5	E	50 - 68
10	X-RAY DIFFRACTION	5	F	50 - 68
11	X-RAY DIFFRACTION	6	E	69 - 86
12	X-RAY DIFFRACTION	6	F	69 - 86
13	X-RAY DIFFRACTION	7	E	87 - 109
14	X-RAY DIFFRACTION	7	F	87 - 109
15	X-RAY DIFFRACTION	8	E	110 - 158
16	X-RAY DIFFRACTION	8	F	110 - 158

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