PDB-4ot1: Structural Basis for the Recognition of Human Cytomegalovirus Gly...

ID or keywords:

Entry

Database: PDB / ID: 4ot1

Title

Structural Basis for the Recognition of Human Cytomegalovirus Glycoprotein B by the Neutralizing Human Antibody SM5-1

Components

Envelope glycoprotein B
SM5-1 Fab Heavy Chain
SM5-1 Fab Light Chain

Keywords

VIRAL PROTEIN/IMMUNE SYSTEM / Immunoglobulin / PH domain / Antibody-Antigen Recognition / VIRAL PROTEIN-IMMUNE SYSTEM complex

Function / homology

Function and homology information

host cell Golgi membrane / host cell endosome membrane / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function

Biological species

Human Cytomegalovirus

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.11 Å

Authors

Diestel, U. / Muller, Y.A.

Citation

Journal: Plos Pathog. / Year: 2014
Title: Structural basis for the recognition of human cytomegalovirus glycoprotein B by a neutralizing human antibody.
Authors: Spindler, N. / Diestel, U. / Stump, J.D. / Wiegers, A.K. / Winkler, T.H. / Sticht, H. / Mach, M. / Muller, Y.A.

History

Deposition	Feb 13, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 13, 2014	Provider: repository / Type: Initial release
Revision 1.1	Oct 22, 2014	Group: Database references
Revision 1.2	Aug 23, 2017	Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ot1.cif.gz	225.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4ot1.ent.gz	189 KB	Display	PDB format
PDBx/mmJSON format	4ot1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4ot1_validation.pdf.gz	463.7 KB	Display	wwPDB validaton report
Full document	4ot1_full_validation.pdf.gz	466.6 KB	Display
Data in XML	4ot1_validation.xml.gz	24 KB	Display
Data in CIF	4ot1_validation.cif.gz	34.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ot/4ot1 ftp://data.pdbj.org/pub/pdb/validation_reports/ot/4ot1	HTTPS FTP

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Related structure data

Related structure data	4osuC 4osn C: citing same article (ref.)
Similar structure data	6svl-4 1fbi-2 5tz2-d 6d2p-d 3rkd-2 4tsb-d 4yxh-d 6ktr-2 6ktr-1 1yjd-d 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	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: Envelope glycoprotein B

H: SM5-1 Fab Heavy Chain

L: SM5-1 Fab Light Chain

hetero molecules

62.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	43.071, 69.411, 100.991
Angle α, β, γ (deg.)	90.00, 99.68, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 1 molecules A

#1: Protein	Envelope glycoprotein B / gB / Glycoprotein GP55 Mass: 14427.061 Da / Num. of mol.: 1 / Fragment: UNP residues 113-133, 344-438 / Mutation: I397A, N398A Source method: isolated from a genetically manipulated source Details: 4-RESIDUE LINKER BETWEEN A133 AND A344 / Source: (gene. exp.) Human Cytomegalovirus / Strain: Towne / Gene: gB, UL55 / Production host: Escherichia coli (E. coli) / Strain (production host): DH10B / References: UniProt: P13201

#1: Protein

Envelope glycoprotein B / gB / Glycoprotein GP55

Mass: 14427.061 Da / Num. of mol.: 1 / Fragment: UNP residues 113-133, 344-438 / Mutation: I397A, N398A
Source method: isolated from a genetically manipulated source
Details: 4-RESIDUE LINKER BETWEEN A133 AND A344 / Source: (gene. exp.)

Human Cytomegalovirus / Strain: Towne / Gene: gB, UL55 / Production host:

Escherichia coli (E. coli) / Strain (production host): DH10B / References: UniProt: P13201

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Antibody , 2 types, 2 molecules HL

#2: Antibody	SM5-1 Fab Heavy Chain Mass: 24878.018 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human)
#3: Antibody	SM5-1 Fab Light Chain Mass: 22569.090 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human)

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Non-polymers , 3 types, 252 molecules

#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.4 Å³/Da / Density % sol: 48.78 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2M L-Proline, 0.1M HEPES, 24% (w/v) Polyethylene glycol 1500, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Dec 15, 2012
Radiation	Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 2.11→42.46 Å / Num. all: 33874 / Num. obs: 31875 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3
Reflection shell	Resolution: 2.11→2.16 Å / % possible all: 98.6

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Processing

Software

Name	Version	Classification
mx	CuBE	data collection
PHASER		phasing
REFMAC	5.7.0032	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.11→42.46 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.933 / SU B: 11.113 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23051	1678	5 %	RANDOM
R_work	0.17134	-	-	-
obs	0.17434	31875	98.46 %	-
all	-	33874	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 38.396 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.55 Å²	0 Å²	0.76 Å²
2-	-	-2.22 Å²	-0 Å²
3-	-	-	0.39 Å²

Refinement step

Cycle: LAST / Resolution: 2.11→42.46 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4181	0	27	248	4456

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.02	4365
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	4020
X-RAY DIFFRACTION	r_angle_refined_deg	1.844	1.954	5956
X-RAY DIFFRACTION	r_angle_other_deg	0.798	3	9323
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.009	5	582
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.665	24.658	161
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.744	15	694
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.1	15	15
X-RAY DIFFRACTION	r_chiral_restr	0.128	0.2	679
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	4988
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	957
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	1.606	2.338	2262
X-RAY DIFFRACTION	r_mcbond_other	1.606	2.337	2261
X-RAY DIFFRACTION	r_mcangle_it	2.337	3.497	2830
X-RAY DIFFRACTION	r_mcangle_other	1.142	1.495	2831
X-RAY DIFFRACTION	r_scbond_it	2.13	2.54	2103
X-RAY DIFFRACTION	r_scbond_other	1.098	1.112	2105
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.677	1.623	3118
X-RAY DIFFRACTION	r_long_range_B_refined	7	8.628	4960
X-RAY DIFFRACTION	r_long_range_B_other	7	8.632	4961
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.11→2.162 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.279	123	-
R_work	0.24	2345	-
obs	-	-	98.56 %

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	3.2807	-2.3127	-1.674	3.9318	2.7781	2.0218	-0.1386	-0.177	-0.3231	0.1384	0.0375	0.0921	0.0646	-0.0445	0.1011	0.1556	0.0588	0.0382	0.1354	0.0292	0.1213	-5.069	3.587	170.569
2	2.2681	-0.339	2.8412	2.7379	-1.121	4.1171	0.1526	-0.0678	-0.0745	-0.0432	0.1601	0.1797	0.267	-0.1537	-0.3127	0.1408	-0.0141	0.0288	0.0674	-0.0023	0.1966	-3.417	-5.799	161.4
3	1.4397	-2.7974	1.0019	5.6324	-2.388	1.7044	-0.1218	0.0006	-0.0169	0.2632	0.0482	-0.0082	-0.1617	-0.1527	0.0736	0.106	-0.0326	0.0247	0.1394	0.0293	0.1835	-7.212	-1.278	164.52
4	3.4173	-0.1373	0.11	0.1984	0.2514	1.1582	-0.1719	-0.104	-0.2326	0.0331	0.0326	0.0015	-0.1462	-0.0244	0.1393	0.1756	0.0205	0.0368	0.0769	0.021	0.1072	0.943	8.041	166.732
5	9.4088	-0.8232	-0.7501	1.3638	1.0791	0.8579	-0.1706	0.2671	-0.3609	0.0128	0.1518	0.0208	-0.007	0.1098	0.0189	0.1388	0.0234	0.0477	0.1144	0.0245	0.1422	6.227	3.038	162.214
6	0.8448	0.6871	-0.7349	1.0928	-0.357	2.4312	-0.1334	0.0038	0.0858	-0.1856	0.0832	0.181	-0.0978	-0.2073	0.0502	0.1603	0.0434	0.0256	0.1111	-0.0065	0.1375	-19.958	15.391	136.194
7	0.505	0.3688	0.1249	1.442	0.5048	3.1261	-0.0878	-0.0462	-0.0621	-0.1668	-0.0489	-0.0967	-0.152	0.0144	0.1367	0.1432	0.0056	0.0306	0.086	0.0048	0.155	-11.118	9.408	138.567
8	3.1214	0.6042	-1.8919	0.206	-0.2504	2.0623	-0.0306	0.0474	0.1521	-0.0252	-0.0071	-0.0426	-0.1718	-0.0388	0.0377	0.178	0.0074	0.0118	0.0756	0.0162	0.165	-11.151	17.584	136.945
9	0.1272	-0.0435	0.297	0.1332	0.1469	1.4074	-0.0124	-0.0519	-0.0092	-0.0574	0.0198	-0.0281	-0.0818	-0.0458	-0.0074	0.1824	-0.0152	0.0633	0.0655	0.0083	0.1603	-16.353	6.891	124.872
10	0.213	-0.7862	-0.3826	3.1163	1.2636	0.8875	-0.0728	0.0008	-0.0932	0.4278	-0.0251	0.423	0.1438	-0.0205	0.0979	0.2909	-0.0417	0.1125	0.0338	0.0415	0.1814	-22.592	7.315	106.291
11	0.27	0.4288	0.9934	3.2502	1.5774	3.7498	0.0264	-0.0014	0.0078	0.0721	-0.0343	0.4268	0.0008	0.0057	0.0079	0.1084	-0.007	0.0671	0.0248	0.0141	0.1904	-22.722	7.733	97.922
12	2.7233	-0.6424	4.6079	1.0028	-2.3259	9.603	-0.1009	0.1619	0.1846	-0.01	-0.1867	-0.0432	-0.1223	0.5001	0.2876	0.0935	-0.022	0.0551	0.1086	-0.0718	0.2036	-4.572	-5.84	135.282
13	0.4233	0.0103	0.4785	1.7102	0.6124	1.1602	-0.0222	-0.0863	0.0058	-0.0893	0.0294	-0.0293	0.0739	-0.1172	-0.0072	0.1652	-0.0342	0.0364	0.102	0.0211	0.1089	-18.26	-10.713	136.811
14	0.0762	0.1087	0.0103	0.5172	0.6047	1.3828	0.0221	-0.0045	-0.0068	-0.0287	0.0493	-0.0889	0.1572	0.0086	-0.0713	0.2026	-0.0243	0.0423	0.0609	0.0005	0.1566	-14.048	-8.147	127.796
15	0.932	0.2989	-0.9192	3.4895	-0.9156	1.067	0.1281	0.0023	0.1287	0.0998	-0.1251	-0.3993	-0.0775	0.0074	-0.0029	0.1859	-0.0399	0.0026	0.0572	0.039	0.1658	-10.839	-1.76	103.604
16	2.3491	2.7052	-1.5708	5.2956	-2.6735	1.4636	-0.179	0.1465	-0.1449	-0.1635	-0.0663	-0.7586	0.1528	-0.0036	0.2453	0.1974	0.007	0.0151	0.0615	0.055	0.3086	-6.307	-8.294	98.295

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	119 - 354
2	X-RAY DIFFRACTION	2	A	355 - 369
3	X-RAY DIFFRACTION	3	A	370 - 383
4	X-RAY DIFFRACTION	4	A	384 - 428
5	X-RAY DIFFRACTION	5	A	429 - 437
6	X-RAY DIFFRACTION	6	H	1 - 33
7	X-RAY DIFFRACTION	7	H	34 - 62
8	X-RAY DIFFRACTION	8	H	63 - 87
9	X-RAY DIFFRACTION	9	H	88 - 161
10	X-RAY DIFFRACTION	10	H	162 - 189
11	X-RAY DIFFRACTION	11	H	190 - 232
12	X-RAY DIFFRACTION	12	L	1 - 6
13	X-RAY DIFFRACTION	13	L	7 - 88
14	X-RAY DIFFRACTION	14	L	89 - 118
15	X-RAY DIFFRACTION	15	L	119 - 188
16	X-RAY DIFFRACTION	16	L	189 - 214

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