PDB-3hr5: M1prime peptide from IgE bound by humanized antibody 47H4 Fab

ID or keywords:

Entry

Database: PDB / ID: 3hr5

Title

M1prime peptide from IgE bound by humanized antibody 47H4 Fab

Components

Fab h47H4 heavy chain
Fab h47H4 light chain
M1prime-derived peptide

Keywords

IMMUNE SYSTEM / Fab-peptide complex

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Eigenbrot, C.W. / Ultsch, M.H.

Citation

Journal: J.Clin.Invest. / Year: 2010
Title: Antibodies specific for a segment of human membrane IgE deplete IgE-producing B cells in humanized mice.
Authors: Brightbill, H.D. / Jeet, S. / Lin, Z. / Yan, D. / Zhou, M. / Tan, M. / Nguyen, A. / Yeh, S. / Delarosa, D. / Leong, S.R. / Wong, T. / Chen, Y. / Ultsch, M. / Luis, E. / Ramani, S.R. / ...

History

Deposition	Jun 8, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 19, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3hr5.cif.gz	349.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3hr5.ent.gz	295.4 KB	Display	PDB format
PDBx/mmJSON format	3hr5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3hr5_validation.pdf.gz	517.8 KB	Display	wwPDB validaton report
Full document	3hr5_full_validation.pdf.gz	553.6 KB	Display
Data in XML	3hr5_validation.xml.gz	66.1 KB	Display
Data in CIF	3hr5_validation.cif.gz	91.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hr/3hr5 ftp://data.pdbj.org/pub/pdb/validation_reports/hr/3hr5	HTTPS FTP

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Related structure data

Similar structure data	5mp3-2 4lkc-d 5ye4-2 6wrp-d 6azm-2 1q9l-1 1l7t-d 1nd0-4 5mv3-5 5tdo-2 6dwa-1 5mv3-3 3okm-d 1f8t-d 2g2r-2 5vzr-1 5b4m-2 2r23-d 3pp3-2 6gxx-d 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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

Similar structure data

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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

L: Fab h47H4 light chain

H: Fab h47H4 heavy chain

A: Fab h47H4 light chain

B: Fab h47H4 heavy chain

P: Fab h47H4 light chain

I: Fab h47H4 heavy chain

Q: Fab h47H4 light chain

J: Fab h47H4 heavy chain

R: M1prime-derived peptide

S: M1prime-derived peptide

T: M1prime-derived peptide

V: M1prime-derived peptide

hetero molecules

208 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Q: Fab h47H4 light chain

J: Fab h47H4 heavy chain

V: M1prime-derived peptide

hetero molecules

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

2

L: Fab h47H4 light chain

H: Fab h47H4 heavy chain

R: M1prime-derived peptide

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

3

A: Fab h47H4 light chain

B: Fab h47H4 heavy chain

S: M1prime-derived peptide

hetero molecules

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

4

P: Fab h47H4 light chain

I: Fab h47H4 heavy chain

T: M1prime-derived peptide

hetero molecules

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

5

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	64.764, 183.824, 194.918
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	L
2	1	A
3	1	P
4	1	Q
1	2	H
2	2	B
3	2	I
4	2	J
1	3	R
2	3	S
3	3	T
4	3	V

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	4	L	3 - 108
2	1	1	4	A	3 - 108
3	1	1	4	P	3 - 108
4	1	1	4	Q	3 - 108
1	2	1	4	L	116 - 215
2	2	1	4	A	116 - 215
3	2	1	4	P	116 - 215
4	2	1	4	Q	116 - 215
1	1	2	4	H	3 - 115
2	1	2	4	B	3 - 115
3	1	2	4	I	3 - 115
4	1	2	4	J	3 - 115
1	2	2	4	H	122 - 215
2	2	2	4	B	122 - 215
3	2	2	4	I	122 - 215
4	2	2	4	J	122 - 215
1	1	3	4	R	1 - 7
2	1	3	4	S	1 - 7
3	1	3	4	T	1 - 7
4	1	3	4	V	1 - 7

NCS ensembles :

ID
1
2
3

#1: Antibody	Fab h47H4 light chain Mass: 24114.795 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody	Fab h47H4 heavy chain Mass: 24121.939 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Protein/peptide	M1prime-derived peptide Mass: 3697.114 Da / Num. of mol.: 4 / Source method: obtained synthetically Details: Residues numbered 9-43 are from the GENBANK accession AAB20659
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.79 Å³/Da / Density % sol: 55.96 %
Crystal grow	Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 5.7 Details: PEG 3350, 0.2 M Ammonium sulfate, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

Diffraction	Mean temperature: 110 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9792 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 7, 2007
Radiation	Monochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.4→50 Å / Num. obs: 81785 / % possible obs: 88.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 4 % / R_merge(I) obs: 0.08 / Net I/σ(I): 15

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
REFMAC	5.2.0019	refinement
HKL-2000		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.4→50 Å / Cor.coef. F_o:F_c: 0.932 / Cor.coef. F_o:F_c free: 0.909 / SU B: 16.383 / SU ML: 0.19 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.409 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25329	1040	1.3 %	RANDOM
R_work	0.21335	-	-	-
all	0.21387	-	-	-
obs	0.21387	80729	88.97 %	-

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: 40.648 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.7 Å²	0 Å²	0 Å²
2-	-	3.8 Å²	0 Å²
3-	-	-	-3.09 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13695	0	24	312	14031

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	14184
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.394	1.949	19337
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.803	5	1815
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.078	24.316	570
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.835	15	2246
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.747	15	62
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	2172
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	10754
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.211	0.2	5785
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.3	0.2	9241
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.148	0.2	638
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	0.246	0.2	63
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.107	0.2	15
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	2.239	2.5	9238
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	3.449	5	14644
X-RAY DIFFRACTION	r_scbond_it	2.726	2.5	5685
X-RAY DIFFRACTION	r_scangle_it	3.982	5	4693
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	L	1542	medium positional	0.52	0.5
1	2	A	1542	medium positional	1.46	0.5
1	3	P	1542	medium positional	0.67	0.5
1	4	Q	1542	medium positional	0.79	0.5
2	1	H	1536	medium positional	0.51	0.5
2	2	B	1536	medium positional	1.17	0.5
2	3	I	1536	medium positional	0.49	0.5
2	4	J	1536	medium positional	0.78	0.5
3	1	R	55	medium positional	0.19	0.5
3	2	S	55	medium positional	0.22	0.5
3	3	T	55	medium positional	0.21	0.5
3	4	V	55	medium positional	0.15	0.5
1	1	L	1542	medium thermal	0.87	2
1	2	A	1542	medium thermal	0.98	2
1	3	P	1542	medium thermal	0.93	2
1	4	Q	1542	medium thermal	0.84	2
2	1	H	1536	medium thermal	0.95	2
2	2	B	1536	medium thermal	0.93	2
2	3	I	1536	medium thermal	0.83	2
2	4	J	1536	medium thermal	0.9	2
3	1	R	55	medium thermal	0.8	2
3	2	S	55	medium thermal	0.85	2
3	3	T	55	medium thermal	0.64	2
3	4	V	55	medium thermal	0.62	2

LS refinement shell

Resolution: 2.4→2.53 Å / Total num. of bins used: 10

	R_factor	Num. reflection	% reflection
R_free	0.394	129	-
R_work	0.278	9798	-
obs	-	-	75.25 %

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	0.3562	0.278	-0.4307	1.4056	-0.5244	1.2771	-0.0586	-0.1231	-0.0326	0.0523	0.1327	0.045	0.0484	-0.0252	-0.0741	-0.1626	0.0044	0.0652	0.0118	0.0364	-0.0712	-18.6282	10.217	0.5457
2	1.1815	-0.6811	-0.638	0.7799	0.4949	0.6896	-0.0714	-0.146	0.0277	-0.0396	0.044	-0.0581	0.0232	0.1153	0.0274	-0.0829	0.0038	0.0002	-0.0291	-0.0568	-0.1525	-5.7271	42.3517	6.6755
3	0.483	-0.2086	0.0668	0.853	0.013	1.5074	0.0135	0.0615	-0.0037	-0.1616	0.0694	-0.0623	0.1267	0.3448	-0.0829	-0.1244	0.0016	0.0421	0.0068	-0.0749	-0.1239	17.091	14.9374	-35.666
4	1.1274	0.0022	-0.6886	1.4006	-0.7629	2.2349	-0.0069	0.156	0.2947	-0.1177	0.1039	0.0314	-0.5372	-0.3957	-0.0971	0.1307	0.0001	-0.0517	-0.0072	0.0135	0.0055	-0.7117	45.2496	-37.3927
5	0.1871	-0.186	-0.2202	0.6127	0.0891	0.6735	0.0919	-0.0105	-0.2129	-0.0576	-0.0535	0.0039	0.4168	-0.0309	-0.0383	0.0872	0.0198	-0.0833	0.0254	0.034	0.0531	14.1233	-15.3074	-6.7088
6	0.9228	-0.2502	-0.0014	1.0312	-0.1524	1.5941	0.0242	0.0017	-0.0793	0.1182	0.125	0.2725	0.0683	-0.1284	-0.1492	-0.1754	0.0416	0.0185	0.0159	0.117	-0.0577	11.0532	1.845	24.0625
7	0.2151	0.1968	-0.311	0.8768	0.1659	1.0864	0.1261	-0.0157	-0.1651	0.0252	0.0133	-0.0051	0.2244	-0.0972	-0.1393	0.1108	-0.068	-0.043	-0.0706	-0.0383	0.0262	-14.5333	-14.2181	-32.8671
8	0.9999	0.0341	0.3471	1.2895	0.1519	1.3013	-0.0081	0.0501	-0.0886	0.1017	-0.0075	0.2733	0.0843	-0.0212	0.0157	-0.1151	-0.0297	0.0245	-0.0362	-0.0622	-0.0898	-11.2183	7.4702	-60.191

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	B	1 - 120
2	X-RAY DIFFRACTION	1	A	1 - 110
3	X-RAY DIFFRACTION	1	S	6 - 12
4	X-RAY DIFFRACTION	2	B	121 - 220
5	X-RAY DIFFRACTION	2	A	111 - 219
6	X-RAY DIFFRACTION	3	H	1 - 120
7	X-RAY DIFFRACTION	3	L	1 - 110
8	X-RAY DIFFRACTION	3	R	7 - 12
9	X-RAY DIFFRACTION	4	H	121 - 220
10	X-RAY DIFFRACTION	4	L	111 - 219
11	X-RAY DIFFRACTION	5	I	1 - 120
12	X-RAY DIFFRACTION	5	P	1 - 110
13	X-RAY DIFFRACTION	5	T	7 - 12
14	X-RAY DIFFRACTION	6	I	121 - 220
15	X-RAY DIFFRACTION	6	P	111 - 219
16	X-RAY DIFFRACTION	7	J	1 - 120
17	X-RAY DIFFRACTION	7	Q	1 - 110
18	X-RAY DIFFRACTION	7	V	7 - 12
19	X-RAY DIFFRACTION	8	J	121 - 220
20	X-RAY DIFFRACTION	8	Q	111 - 219

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