PDB-3qhz: Crystal Structure of human anti-influenza Fab 2D1

ID or keywords:

Entry

Database: PDB / ID: 3qhz

Title

Crystal Structure of human anti-influenza Fab 2D1

Components

Human monoclonal antibody del2D1, Fab Heavy Chain
Human monoclonal antibody del2D1, Fab Light Chain

Keywords

IMMUNE SYSTEM / Immunoglobulin / Immune recognition / Influenza A hemagglutinin

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.55 Å

Authors

Ekiert, D.C. / Wilson, I.A.

Citation

Journal: MBio / Year: 2011
Title: An insertion mutation that distorts antibody binding site architecture enhances function of a human antibody.
Authors: Krause, J.C. / Ekiert, D.C. / Tumpey, T.M. / Smith, P.B. / Wilson, I.A. / Crowe, J.E.

History

Deposition	Jan 26, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 16, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 2.0	Dec 25, 2019	Group: Derived calculations / Polymer sequence Category: entity_poly / pdbx_struct_mod_residue / struct_conn Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1	Sep 13, 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3qhz.cif.gz	360.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3qhz.ent.gz	293.5 KB	Display	PDB format
PDBx/mmJSON format	3qhz.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3qhz_validation.pdf.gz	454.6 KB	Display	wwPDB validaton report
Full document	3qhz_full_validation.pdf.gz	462.7 KB	Display
Data in XML	3qhz_validation.xml.gz	42.3 KB	Display
Data in CIF	3qhz_validation.cif.gz	63.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qh/3qhz ftp://data.pdbj.org/pub/pdb/validation_reports/qh/3qhz	HTTPS FTP

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Related structure data

Related structure data	3qhfC 3lzfS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4r7n-8 6w5d-1 1nd0-6 4odu-2 1ynl-d 4yx2-2 5m6a-2 2fbj-d 6dca-1 6c5k-2 5ig7-2 5t4z-2 6nb5-2 5bk5-4 2f5a-d 4xbe-d 4xbg-2 5ud9-d 5cp7-3 1dqq-2 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

Related structure data

3qhfC

3lzfS

C: citing same article (ref.)

S: Starting model for refinement

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

H: Human monoclonal antibody del2D1, Fab Heavy Chain

L: Human monoclonal antibody del2D1, Fab Light Chain

I: Human monoclonal antibody del2D1, Fab Heavy Chain

M: Human monoclonal antibody del2D1, Fab Light Chain

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

1

H: Human monoclonal antibody del2D1, Fab Heavy Chain

L: Human monoclonal antibody del2D1, Fab Light Chain

defined by author&software
47.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

I: Human monoclonal antibody del2D1, Fab Heavy Chain

M: Human monoclonal antibody del2D1, Fab Light Chain

defined by author&software
47.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	69.920, 80.940, 77.195
Angle α, β, γ (deg.)	90.00, 100.14, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Antibody	Human monoclonal antibody del2D1, Fab Heavy Chain Mass: 24970.133 Da / Num. of mol.: 2 / Fragment: Fab Heavy Chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Immunoglobulin gamma / Plasmid: pEE6.4 / Cell line (production host): 293F / Production host: Homo sapiens (human)
#2: Antibody	Human monoclonal antibody del2D1, Fab Light Chain Mass: 22812.109 Da / Num. of mol.: 2 / Fragment: Fab Light Chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Immunoglobulin lambda / Plasmid: pEE12.4 / Cell line (production host): 293F / Production host: Homo sapiens (human)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 939 / 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: 2.25 Å³/Da / Density % sol: 45.33 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion Details: 22% PEG 4000 and 150 mM calcium acetate, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction	Mean temperature: 80 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97 Å
Detector	Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 15, 2010
Radiation	Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97 Å / Relative weight: 1
Reflection	Resolution: 1.55→50 Å / Num. obs: 121518 / % possible obs: 98.7 %
Reflection shell	Resolution: 1.55→1.58 Å / % possible all: 96.5

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Processing

Software

Name	Version	Classification
Blu-Ice		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.6.4_486)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3LZF (chains H and L)

3lzf

Resolution: 1.55→28.085 Å / SU ML: 0.19 / σ(F): 1.33 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2062	6065	5.01 %	Random
R_work	0.1796	-	-	-
obs	0.1809	120972	98.64 %	-

Solvent computation

Shrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 43.464 Å² / k_sol: 0.423 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.3363 Å²	0 Å²	0.1481 Å²
2-	-	0.0342 Å²	0 Å²
3-	-	-	3.3021 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→28.085 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6469	0	0	939	7408

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	6909
X-RAY DIFFRACTION	f_angle_d	1.077	9488
X-RAY DIFFRACTION	f_dihedral_angle_d	11.368	2487
X-RAY DIFFRACTION	f_chiral_restr	0.062	1107
X-RAY DIFFRACTION	f_plane_restr	0.006	1214

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 (%)
1.55-1.5676	0.3087	183	0.3179	3719	X-RAY DIFFRACTION	97
1.5676-1.5861	0.3534	198	0.3181	3687	X-RAY DIFFRACTION	95
1.5861-1.6054	0.3587	215	0.2991	3680	X-RAY DIFFRACTION	96
1.6054-1.6257	0.2853	198	0.2543	3692	X-RAY DIFFRACTION	95
1.6257-1.6471	0.289	199	0.2331	3657	X-RAY DIFFRACTION	94
1.6471-1.6697	0.2766	199	0.2341	3634	X-RAY DIFFRACTION	95
1.6697-1.6935	0.2727	224	0.2371	3786	X-RAY DIFFRACTION	98
1.6935-1.7188	0.2237	193	0.2106	3825	X-RAY DIFFRACTION	99
1.7188-1.7457	0.2337	198	0.2087	3846	X-RAY DIFFRACTION	99
1.7457-1.7743	0.2514	191	0.2075	3872	X-RAY DIFFRACTION	100
1.7743-1.8049	0.2541	193	0.2219	3882	X-RAY DIFFRACTION	100
1.8049-1.8377	0.2194	204	0.2023	3886	X-RAY DIFFRACTION	100
1.8377-1.873	0.2367	201	0.2023	3837	X-RAY DIFFRACTION	100
1.873-1.9112	0.2085	203	0.1972	3849	X-RAY DIFFRACTION	100
1.9112-1.9528	0.241	226	0.2092	3861	X-RAY DIFFRACTION	100
1.9528-1.9982	0.1954	200	0.1799	3893	X-RAY DIFFRACTION	100
1.9982-2.0482	0.1902	205	0.1759	3867	X-RAY DIFFRACTION	100
2.0482-2.1035	0.2244	177	0.1919	3931	X-RAY DIFFRACTION	100
2.1035-2.1654	0.2253	205	0.1768	3831	X-RAY DIFFRACTION	100
2.1654-2.2353	0.1862	205	0.1688	3895	X-RAY DIFFRACTION	100
2.2353-2.3151	0.2096	219	0.1793	3873	X-RAY DIFFRACTION	100
2.3151-2.4078	0.1951	232	0.1716	3844	X-RAY DIFFRACTION	100
2.4078-2.5173	0.2036	180	0.167	3888	X-RAY DIFFRACTION	100
2.5173-2.6499	0.18	220	0.1715	3884	X-RAY DIFFRACTION	100
2.6499-2.8158	0.2102	194	0.1714	3924	X-RAY DIFFRACTION	100
2.8158-3.0329	0.1863	198	0.1665	3895	X-RAY DIFFRACTION	100
3.0329-3.3377	0.1898	224	0.1715	3895	X-RAY DIFFRACTION	100
3.3377-3.8197	0.2036	196	0.1655	3894	X-RAY DIFFRACTION	99
3.8197-4.8084	0.1532	184	0.1367	3867	X-RAY DIFFRACTION	98
4.8084-28.0901	0.2083	201	0.1846	3813	X-RAY DIFFRACTION	95

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	0.9674	-0.4976	-0.3637	1.3934	-0.3554	0.8201	-0.0395	0.0641	-0.067	-0.1451	0.0357	0.0513	0.0242	-0.0865	0.0102	0.2629	-0.001	-0.0008	0.0307	-0.004	0.0309	-7.976	-25.5792	44.8558
2	1.2639	0.522	0.026	1.2626	0.0652	0.6357	0.0301	0.0381	0.2205	0.0166	-0.0393	0.2826	-0.0524	-0.0666	0.0057	0.3017	0.0337	0.0012	0.1029	0.0008	0.1471	-17.8004	-20.2557	74.9023
3	0.2863	0.1513	0.2435	2.0169	-0.0829	0.3132	-0.0038	0.0031	0.0082	-0.086	-0.0334	-0.08	-0.035	-0.0234	0.0271	0.3084	0.013	0.0033	0.0511	-0.0014	0.0412	-8.6957	-4.3471	42.2603
4	0.7008	0.0111	-0.1043	3.0653	0.1217	0.9157	0.0118	-0.0252	-0.0149	0.0171	0.0095	-0.1779	0.0538	-0.0509	-0.0304	0.2697	-0.0054	0.0306	0.0612	0.0189	0.0531	-9.1574	-7.6401	80.439
5	0.8116	-0.0355	-0.295	0.7668	0.0976	1.075	-0.122	-0.0147	0.0114	0.034	0.1	0.0305	-0.07	-0.0836	0.0394	0.3095	-0.0037	-0.024	0.1013	-0.02	0.0848	23.0231	5.0115	69.1011
6	0.864	-0.0441	0.602	1.5173	0.4377	1.0715	0.0472	-0.0621	-0.0544	-0.2319	-0.028	-0.0288	-0.1166	-0.1969	-0.0099	0.3055	-0.0169	-0.0238	0.0892	-0.005	0.0477	22.8761	0.3403	38.3484
7	0.9484	0.36	0.0199	3.8912	-0.6682	0.2207	0.0516	-0.0864	0.0525	0.4255	-0.0186	0.1058	-0.0613	-0.0502	-0.0378	0.2596	-0.0216	0.008	0.0733	-0.0096	0.0538	21.0466	-16.0539	71.5693
8	0.6308	-0.4409	-0.0641	1.3438	0.2998	0.6435	0.0704	0.0353	0.0301	-0.0933	0.0063	-0.0311	0.0829	-0.0451	-0.0631	0.3608	-0.025	-0.0156	0.07	0.0116	0.0509	33.2961	-12.677	35.6546

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain H and (resid 1:127)
2	X-RAY DIFFRACTION	2	chain H and (resid 128:250)
3	X-RAY DIFFRACTION	3	chain L and (resid 1:112)
4	X-RAY DIFFRACTION	4	chain L and (resid 113:250)
5	X-RAY DIFFRACTION	5	chain I and (resid 1:127)
6	X-RAY DIFFRACTION	6	chain I and (resid 128:250)
7	X-RAY DIFFRACTION	7	chain M and (resid 1:112)
8	X-RAY DIFFRACTION	8	chain M and (resid 113:250)

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