PDB-7jz4: Crystal structure of broadly Plasmodium RIFIN reactive LAIR1-inse...

ID or keywords:

Entry

Database: PDB / ID: 7jz4

Title

Crystal structure of broadly Plasmodium RIFIN reactive LAIR1-inserted antibody MGD21

Components

MGD21 heavy chain
MGD21 light chain

Keywords

IMMUNE SYSTEM /

LAIR1 / insertion /

antibody / RIFIN /

Malaria

Function / homology

PHOSPHATE ION

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.747 Å

Authors

Xu, K. / Kwong, P.D.

Citation

Journal: Nat Commun / Year: 2021
Title: Structural basis of LAIR1 targeting by polymorphic Plasmodium RIFINs.
Authors: Xu, K. / Wang, Y. / Shen, C.H. / Chen, Y. / Zhang, B. / Liu, K. / Tsybovsky, Y. / Wang, S. / Farney, S.K. / Gorman, J. / Stephens, T. / Verardi, R. / Yang, Y. / Zhou, T. / Chuang, G.Y. / ...

History

Deposition	Sep 1, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 26, 2021	Provider: repository / Type: Initial release
Revision 1.1	Sep 22, 2021	Group: Database references / Category: citation / citation_author / database_2 Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jz/7jz4 ftp://data.pdbj.org/pub/pdb/validation_reports/jz/7jz4	HTTPS FTP

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Related structure data

Related structure data	7jz1C 7jziC 7jzkC 3kgrS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5usl-2 1fbi-2 5usl-1 7d85-1 3rcd-5 5en2-d 7chs-d 1fsk-2 3rkd-2 1fsk-4 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

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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: MGD21 heavy chain

B: MGD21 light chain

D: MGD21 light chain

C: MGD21 heavy chain

hetero molecules

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

1

A: MGD21 heavy chain

D: MGD21 light chain

hetero molecules

defined by author&software
Evidence: gel filtration
63.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: MGD21 light chain

C: MGD21 heavy chain

hetero molecules

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

Unit cell

Length a, b, c (Å)	80.932, 81.099, 111.561
Angle α, β, γ (deg.)	90.000, 94.030, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	(chain B and (resid 2 through 3 or resid 5...
2	1	(chain D and (resid 2 through 3 or resid 5...

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details	Auth asym-ID	Auth seq-ID
1	1	1	(chain B and (resid 2 through 3 or resid 5...	B	2 - 3
1	2	1	(chain B and (resid 2 through 3 or resid 5...	B	5 - 24
1	3	1	(chain B and (resid 2 through 3 or resid 5...	B	26 - 123
1	4	1	(chain B and (resid 2 through 3 or resid 5...	B	125 - 143
1	5	1	(chain B and (resid 2 through 3 or resid 5...	B	145 - 152
1	6	1	(chain B and (resid 2 through 3 or resid 5...	B	154 - 160
1	7	1	(chain B and (resid 2 through 3 or resid 5...	B	162 - 169
1	8	1	(chain B and (resid 2 through 3 or resid 5...	B	171 - 187
1	9	1	(chain B and (resid 2 through 3 or resid 5...	B	189 - 190
1	10	1	(chain B and (resid 2 through 3 or resid 5...	B	192 - 214
2	1	1	(chain D and (resid 2 through 3 or resid 5...	D	2 - 3
2	2	1	(chain D and (resid 2 through 3 or resid 5...	D	5 - 24
2	3	1	(chain D and (resid 2 through 3 or resid 5...	D	0
2	4	1	(chain D and (resid 2 through 3 or resid 5...	D	2 - 214
2	5	1	(chain D and (resid 2 through 3 or resid 5...	D	15
2	6	1	(chain D and (resid 2 through 3 or resid 5...	D	162 - 169
2	7	1	(chain D and (resid 2 through 3 or resid 5...	D	0
2	8	1	(chain D and (resid 2 through 3 or resid 5...	D	2 - 214
2	9	1	(chain D and (resid 2 through 3 or resid 5...	D	189 - 190
2	10	1	(chain D and (resid 2 through 3 or resid 5...	D	192 - 214

#1: Antibody

MGD21 heavy chain

Mass: 39403.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Production host:

Homo sapiens (human)

#2: Antibody

MGD21 light chain

Mass: 23200.779 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Production host:

Homo sapiens (human)

#3: Chemical

ChemComp-PO4 / PHOSPHATE ION /

Phosphate

Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO₄

#4: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE /

N-Acetylglucosamine

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

#5: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.92 Å³/Da / Density % sol: 57.83 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M MgCl2, 0.1 M Tris HCl pH 8.5, 20% PEG 3350, 25% PEG 400

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-ID / Wavelength: 1 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 20, 2016

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.747→50 Å / Num. obs: 37579 / % possible obs: 99.9 % / Redundancy: 3.8 % / R_merge(I) obs: 0.103 / R_pim(I) all: 0.061 / R_rim(I) all: 0.12 / Χ²: 1.402 / Net I/σ(I): 10.3

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.747-2.8	3.8	0.872	1893	0.641	0.517	1.015	0.871	99.5
2.8-2.85	3.9	0.71	1817	0.712	0.419	0.825	0.948	99.9
2.85-2.9	3.8	0.564	1874	0.822	0.332	0.655	0.952	99.6
2.9-2.96	3.9	0.49	1861	0.849	0.289	0.57	1.029	100
2.96-3.03	3.8	0.39	1875	0.896	0.23	0.453	1.077	99.7
3.03-3.1	3.8	0.332	1877	0.922	0.197	0.386	1.195	100
3.1-3.17	3.9	0.266	1884	0.946	0.157	0.309	1.364	99.8
3.17-3.26	3.8	0.217	1838	0.959	0.128	0.253	1.469	99.8
3.26-3.36	3.9	0.196	1898	0.959	0.116	0.228	1.577	100
3.36-3.46	3.8	0.166	1860	0.969	0.098	0.193	1.598	99.9
3.46-3.59	3.8	0.143	1849	0.978	0.084	0.166	1.649	99.9
3.59-3.73	3.8	0.126	1879	0.984	0.074	0.147	1.634	99.9
3.73-3.9	3.8	0.124	1881	0.979	0.073	0.144	1.723	99.9
3.9-4.11	3.8	0.11	1885	0.98	0.065	0.129	1.739	100
4.11-4.36	3.8	0.107	1856	0.98	0.063	0.124	1.762	100
4.36-4.7	3.8	0.096	1909	0.984	0.057	0.112	1.641	99.9
4.7-5.17	3.8	0.085	1876	0.988	0.05	0.098	1.609	99.8
5.17-5.92	3.8	0.074	1904	0.989	0.044	0.086	1.493	99.9
5.92-7.46	3.8	0.061	1921	0.993	0.037	0.071	1.405	100
7.46-50	3.6	0.045	1942	0.996	0.028	0.054	1.299	99.3

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Processing

Software

Name	Version	Classification
PHENIX	1.11.1_2575	refinement
SCALEPACK		data scaling
PDB_EXTRACT	3.25	data extraction
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3KGR

3kgr

Resolution: 2.747→38.933 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.88 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2493	1844	4.91 %
R_work	0.1939	35710	-
obs	0.1966	37554	99.19 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 233.89 Å² / B_iso mean: 82.2212 Å² / B_iso min: 30 Å²

Refinement step

Cycle: final / Resolution: 2.747→38.933 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8453	0	53	10	8516
B_iso mean	-	-	154.29	60.89	-
Num. residues	-	-	-	-	1109

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	8704
X-RAY DIFFRACTION	f_angle_d	0.921	11847
X-RAY DIFFRACTION	f_chiral_restr	0.055	1341
X-RAY DIFFRACTION	f_plane_restr	0.008	1519
X-RAY DIFFRACTION	f_dihedral_angle_d	7.203	5206

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	B	1747	X-RAY DIFFRACTION	12.683	TORSIONAL
1	2	D	1747	X-RAY DIFFRACTION	12.683	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2.747-2.8212	0.3814	129	0.3044	2517	91
2.8212-2.9042	0.3154	142	0.2922	2747	100
2.9042-2.9979	0.348	133	0.273	2786	100
2.9979-3.105	0.3471	151	0.2596	2706	100
3.105-3.2292	0.3236	144	0.2444	2752	100
3.2292-3.3761	0.2908	126	0.227	2783	100
3.3761-3.554	0.2742	143	0.2134	2739	100
3.554-3.7765	0.2484	134	0.203	2744	100
3.7765-4.0678	0.2278	150	0.19	2772	100
4.0678-4.4766	0.2228	165	0.1565	2750	100
4.4766-5.1232	0.1967	141	0.1458	2785	100
5.1232-6.4499	0.2231	118	0.1705	2793	100
6.4499-38.933	0.2392	168	0.187	2836	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	0.6448	-0.4051	-0.0377	6.4357	2.5769	2.8635	0.034	0.0754	0.0817	-0.3773	0.1067	0.4776	0.001	-0.0945	-0.1677	0.5228	0.0648	-0.0137	0.5187	0.1553	0.543	-63.9583	-34.709	-44.8906
2	4.4792	-0.6292	-2.3331	3.3223	0.2646	5.1913	-0.1204	0.0862	-0.1579	-0.1551	-0.4572	0.0023	0.2473	0.0017	0.5413	0.5604	-0.0098	0.0583	0.4015	0.0606	0.4195	-65.2826	-47.2522	13.2003
3	5.8431	-0.3201	-0.9706	5.5666	-0.3759	2.5279	-0.1961	-0.2749	0.025	-0.2377	0.0411	-0.3435	0.1501	-0.0582	0.1459	0.4944	-0.078	0.1476	0.6389	-0.2029	0.5113	-88.0072	-46.3373	25.6109
4	4.034	0.2123	-2.3775	1.5157	-0.6227	3.1214	-0.2611	-0.6287	-0.3609	-0.2317	-0.3973	-0.6564	0.2984	1.2814	0.7186	0.6976	0.0946	0.0097	0.941	0.2573	0.6262	-38.9253	-34.8905	-6.6426
5	3.3174	-2.066	0.1154	3.6978	0.1096	2.4835	-0.5591	-0.1958	0.2885	0.4479	0.6278	-0.0375	-0.2762	-0.1922	-0.0595	0.6856	0.0756	0.0658	0.4121	0.0568	0.3254	-48.4563	-74.6112	-33.8977
6	6.0266	3.0683	2.073	6.016	1.1759	4.173	-0.3343	0.6256	-0.1842	-0.1274	0.6287	-0.3814	0.2649	0.7438	-0.27	0.586	0.0729	0.1121	0.4721	-0.0425	0.2852	-34.3105	-92.3323	-43.1138
7	1.4087	-3.2756	-2.047	7.8637	2.8963	2.0057	-0.1906	0.1984	-0.118	0.897	0.0672	0.9098	0.0925	-0.4134	0.1413	0.6075	0.0592	0.0736	0.6477	0.1397	0.7312	-70.5988	-43.1769	-34.1538
8	4.4856	-0.478	-0.2002	7.0626	-1.0365	4.3951	0.4384	0.7309	0.7115	-0.5349	-0.2176	0.6547	-0.7399	-0.6757	-0.1617	0.6026	0.2402	0.0226	0.6527	0.0026	0.5567	-72.4839	-26.8099	3.7554
9	0.5696	0.5743	-0.5736	5.6553	-0.3843	7.1783	0.1522	0.0987	0.0773	-0.0561	-0.5003	0.0679	-0.8042	0.2896	0.3717	0.6905	0.1023	0.0218	0.4967	-0.0078	0.561	-69.2322	-25.4385	12.5094
10	7.0442	2.6722	-2.3062	2.7023	-0.8442	6.6962	0.4068	0.0159	0.2142	-0.4663	-0.6391	0.1459	-0.724	-0.4746	0.2159	0.6817	0.128	-0.066	0.5158	-0.0414	0.4356	-67.908	-29.8834	6.7132
11	6.2391	1.0289	-4.5246	0.7059	-1.8315	5.4512	-0.1887	-0.3826	0.5943	-0.078	0.4477	-0.1409	-0.0185	0.2428	-0.5434	0.9738	-0.0009	0.2242	0.4915	0.0421	0.6097	-55.7537	-16.8212	-5.5873
12	9.5634	-5.5634	-3.7642	5.2001	5.7895	8.7208	0.0113	-0.0686	0.107	-0.2099	0.4361	-1.0339	0.4123	1.9444	-0.2935	0.5492	0.0742	-0.0047	1.02	0.2973	0.7006	-36.4389	-34.2891	-21.0251
13	3.3739	-1.1836	-2.7374	5.3882	4.1515	5.7394	-0.3212	0.0084	-0.3106	0.6678	-0.1689	0.2742	0.1658	0.0783	0.3646	0.6664	0.0315	0.1184	0.4591	0.2397	0.5143	-49.5066	-27.2298	-17.5764
14	2.4978	0.7755	3.3436	1.8096	2.698	6.2068	0.107	0.3261	-0.013	0.2608	-0.0914	0.3	-0.268	0.3852	0.2918	0.857	-0.0237	0.0343	0.6307	0.1929	0.7466	-51.471	-34.541	-23.1104
15	4.2507	-3.3106	0.5009	4.1874	1.5241	2.7881	-0.5985	-1.0474	0.5259	1.1231	-0.991	0.3845	-0.0812	1.7695	0.8863	0.7931	-0.0405	0.0352	0.7849	0.0868	0.7834	-49.468	-20.8709	-3.2877
16	4.7354	-2.903	-1.5075	7.4087	1.4415	5.8562	0.0731	0.6745	-0.0917	-0.1014	-0.4128	-0.3713	0.2277	0.5582	0.4067	0.6582	0.048	0.1695	0.6934	0.2061	0.5954	-45.2667	-30.1506	-26.1112
17	4.6266	-2.0473	-0.6422	5.0921	-0.5224	3.2073	0.3919	0.5399	0.4682	-1.0285	-0.3795	-0.0934	-0.3557	0.1607	-0.0484	0.9173	-0.045	0.0258	0.4876	0.1142	0.4662	-49.1761	-64.8257	-55.3007
18	3.212	-2.6393	-0.1428	8.1536	-0.7574	5.668	0.1036	0.2442	0.2776	-1.3995	0.0956	0.197	0.0456	-0.4799	-0.2493	0.7003	-0.148	-0.0257	0.4598	0.096	0.3689	-54.1952	-69.2854	-52.6069

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'D' and (resid 104 through 214 )	D	104 - 214
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 1 through 118 )	C	1 - 118
3	X-RAY DIFFRACTION	3	chain 'C' and (resid 119 through 235 )	C	119 - 235
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 236 through 351 )	C	236 - 351
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 1 through 128 )	A	1 - 128
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 129 through 232 )	A	129 - 232
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 233 through 362 )	A	233 - 362
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 2 through 39 )	B	2 - 39
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 40 through 76 )	B	40 - 76
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 77 through 103 )	B	77 - 103
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 104 through 114 )	B	104 - 114
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 115 through 129 )	B	115 - 129
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 130 through 151 )	B	130 - 151
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 152 through 164 )	B	152 - 164
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 165 through 175 )	B	165 - 175
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 176 through 214 )	B	176 - 214
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 2 through 39 )	D	2 - 39
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 40 through 103 )	D	40 - 103

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