PDB-6b5p: Structure of PfCSP peptide 20 with human antibody CIS42

ID or keywords:

Entry

Database: PDB / ID: 6b5p

Title

Structure of PfCSP peptide 20 with human antibody CIS42

Components

CIS42 Fab Heavy chain
CIS42 Fab Light chain
pfCSP peptide 20: ASN-PRO-ASP-PRO-ASN-ALA-ASN-PRO-ASN-VAL-ASP

Keywords

IMMUNE SYSTEM /

Malaria / pfCSP /

vaccine /

antibodies

Function / homology

Function and homology information

entry into host cell by a symbiont-containing vacuole / side of membrane /

cell surface /

plasma membrane /

cytoplasm
Similarity search - Function

Biological species

Homo sapiens (human)

Plasmodium falciparum (malaria parasite P. falciparum)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.297 Å

Authors

Pancera, M. / Weidle, C.

Citation

Journal: Nat. Med. / Year: 2018
Title: A human monoclonal antibody prevents malaria infection by targeting a new site of vulnerability on the parasite.
Authors: Kisalu, N.K. / Idris, A.H. / Weidle, C. / Flores-Garcia, Y. / Flynn, B.J. / Sack, B.K. / Murphy, S. / Schon, A. / Freire, E. / Francica, J.R. / Miller, A.B. / Gregory, J. / March, S. / Liao, ...

History

Deposition	Sep 29, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 21, 2018	Provider: repository / Type: Initial release
Revision 1.1	Apr 4, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2	Apr 25, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6b5p.cif.gz	243.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6b5p.ent.gz	209.3 KB	Display	PDB format
PDBx/mmJSON format	6b5p.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b5/6b5p ftp://data.pdbj.org/pub/pdb/validation_reports/b5/6b5p	HTTPS FTP

-
Related structure data

Related structure data	6b5lC 6b5mC 6b5nC 6b5oC 6b5rC 6b5sC 6b5tC C: citing same article (ref.)
Similar structure data	6b5r-d 6db5-2 3mlt-1 2fb4-d 4eow-d 4n8c-1 4n8c-2 3nac-d 2b1a-d 7kfg-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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (2) #21 - Sep 2001 Antibodies similarity (2) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1)

Deposited unit

A: pfCSP peptide 20: ASN-PRO-ASP-PRO-ASN-ALA-ASN-PRO-ASN-VAL-ASP

H: CIS42 Fab Heavy chain

L: CIS42 Fab Light chain

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	41.832, 70.680, 166.733
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein/peptide	pfCSP peptide 20: ASN-PRO-ASP-PRO-ASN-ALA-ASN-PRO-ASN-VAL-ASP Mass: 1166.155 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum) References: UniProt: P02893*PLUS
#2: Antibody	CIS42 Fab Heavy chain Mass: 23617.463 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody	CIS42 Fab Light chain Mass: 22755.172 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.59 Å³/Da / Density % sol: 52.56 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 15% PEG3350, 9% Isopropanol, 0.12M Ammonium Citrate pH 8.5

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 12, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.3→32.537 Å / Num. obs: 18859 / % possible obs: 82.6 % / Redundancy: 5.6 % / Net I/σ(I): 19.8

-
Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Resolution: 2.297→32.537 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2682	977	5.18 %
R_work	0.2367	-	-
obs	0.2383	18856	82.51 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.297→32.537 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3244	0	0	96	3340

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	3335
X-RAY DIFFRACTION	f_angle_d	0.642	4563
X-RAY DIFFRACTION	f_dihedral_angle_d	10.386	1969
X-RAY DIFFRACTION	f_chiral_restr	0.046	518
X-RAY DIFFRACTION	f_plane_restr	0.005	581

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 (%)
2.2973-2.4184	0.3654	49	0.332	1004	X-RAY DIFFRACTION	33
2.4184-2.5699	0.3484	100	0.3176	1838	X-RAY DIFFRACTION	61
2.5699-2.7682	0.3266	145	0.2999	2517	X-RAY DIFFRACTION	83
2.7682-3.0466	0.3109	173	0.2849	3030	X-RAY DIFFRACTION	99
3.0466-3.487	0.3043	167	0.261	3092	X-RAY DIFFRACTION	100
3.487-4.3916	0.2345	175	0.2139	3102	X-RAY DIFFRACTION	100
4.3916-32.5405	0.2195	168	0.1884	3296	X-RAY DIFFRACTION	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	1.2776	-2.6673	0.2172	8.8835	0.5026	0.837	-0.1453	-0.2428	0.1181	0.6672	0.1288	-0.075	-0.0512	-0.1589	-0.0021	0.4556	0.0096	-0.2306	0.4214	-0.0067	0.3207	5.1169	0.3776	9.1151
2	1.4368	-0.1028	0.8161	2.3733	-0.3196	4.2304	0.2337	0.2351	-0.7987	0.0662	-0.283	-0.5737	0.4992	0.3147	-0.047	0.1989	0.0904	-0.0527	0.1672	0.0257	0.3094	-3.3809	-13.5442	-13.3756
3	1.2533	0.1721	0.3699	2.1843	-0.8412	2.9295	0.1331	-0.1964	-0.2483	0.2884	-0.3638	-0.261	0.1389	0.0796	0.0651	0.2617	0.0019	-0.1059	0.1393	0.0996	0.2299	-3.5316	-8.2591	-2.1279
4	1.6707	0.6586	1.6094	2.2753	0.1588	4.2798	0.1004	0.0728	0.0289	0.0652	-0.1933	-0.3478	-0.0137	0.0445	0.1319	0.1929	-0.0153	-0.0123	0.0764	0.0582	0.215	-6.1653	-7.7367	-11.0759
5	2.6176	0.0653	0.4331	2.4493	-2.2076	2.0756	-0.331	0.4205	0.185	-0.3557	0.1919	-0.4274	-0.4326	-0.1818	0.0243	0.5224	-0.0184	-0.0147	0.2122	0.0709	0.2916	-21.0137	-0.4026	-45.8097
6	4.7138	-0.3366	-1.9121	4.783	0.6401	3.7999	0.0454	0.2636	0.1604	-0.3968	0.156	-0.6049	-0.0729	-0.0638	0.4961	0.238	0.0008	-0.1623	0.1283	-0.0714	0.3015	-13.1831	-7.7978	-38.7977
7	2.6683	1.3	-0.22	5.7627	-0.8105	5.8696	0.6286	-0.1061	-0.158	0.6674	-0.3602	-0.4709	-0.8764	0.3817	-0.5036	0.3573	0.1177	0.0104	0.2447	-0.0572	0.2489	-15.7054	-1.6271	-35.8902
8	2.9854	-0.5197	-1.2629	6.2617	-4.3611	3.9332	0.4054	0.8873	0.0409	-1.1917	-0.1396	0.0986	0.461	-0.2429	0.3425	0.5102	0.1339	0.1367	0.393	0.0308	0.191	-15.7325	2.6816	-52.8447
9	2.3067	0.9923	-0.6224	2.744	-0.9269	3.3328	0.1891	0.2344	-0.0536	-1.0293	-0.268	-0.1993	0.9381	0.3548	-0.0006	0.6068	0.0431	0.0122	0.1996	0.028	0.2795	-15.3673	-10.132	-45.4298
10	7.019	-0.795	-3.2938	2.3341	1.0653	6.3461	-0.3528	0.4661	0.5604	0.0869	0.354	0.0965	-0.3323	-0.7992	-0.0269	0.4233	0.0695	-0.0016	0.2545	0.0614	0.3233	-7.0588	18.0367	-12.8358
11	6.0475	0.1956	-0.0586	7.0257	-1.9818	3.5041	-0.255	-0.4838	-0.2396	1.4198	0.3181	0.6512	-0.6689	-0.4615	-0.1518	0.4882	0.0857	-0.0772	0.1798	0.0014	0.2914	-8.3841	15.2714	-1.083
12	3.9912	0.8249	1.1088	3.3172	-1.5509	3.7516	0.1658	-0.0021	-0.2536	0.5037	-0.0864	-0.1339	-0.0854	0.282	-0.0783	0.3224	0.058	-0.1669	0.2113	0.0498	0.2231	0.234	8.3298	-7.6646
13	0.9548	-0.7952	1.2427	0.8149	-0.8864	1.7673	0.2214	0.106	-0.4626	0.1439	-0.1767	-0.2027	0.265	0.3869	-0.287	0.5331	-0.1842	-0.353	0.3283	-0.0099	0.5371	8.5842	13.5767	-6.3703
14	7.3893	1.2249	3.9635	4.2434	0.3095	2.1561	-0.4031	0.5068	0.3764	0.6188	0.3314	-0.0137	-0.7088	0.4314	0.3313	0.6441	-0.0267	-0.0804	0.1499	0.0812	0.2208	-0.8928	19.286	-4.1685
15	3.1457	0.8365	0.0024	4.4884	-1.0175	2.7553	-0.4565	0.3894	-0.004	0.143	0.1103	-0.0618	-0.6552	0.1895	-0.043	0.2451	-0.0954	-0.0534	0.2357	0.0163	0.2325	-0.8887	12.5793	-13.1365
16	2.4269	-2.887	2.7274	4.2822	-3.3344	3.1196	-0.2048	-0.2171	0.2134	0.6816	0.2491	-0.1264	-0.7254	-0.2356	-0.2922	0.4787	0.0058	0.0234	0.1747	0.0101	0.2251	-6.5105	3.4959	1.3578
17	0.6097	-0.6509	0.1151	1.5716	0.336	1.9721	-0.4752	0.6705	0.3453	0.1662	-0.2811	-0.0609	-0.6504	0.9396	-0.8829	0.2412	-0.1308	-0.2322	0.4041	0.1503	0.2792	-7.8645	18.3015	-26.4206
18	5.1017	4.0978	-0.7975	8.4193	-1.0695	3.7449	0.0043	0.0697	-0.6154	-0.7637	0.4023	0.0365	0.5672	-0.6251	-0.3502	0.3075	-0.0741	-0.1334	0.3508	0.0569	0.4929	-28.8032	-0.7508	-42.942
19	4.6688	1.2012	1.5596	1.1926	0.0585	2.8952	0.0693	0.1205	0.4982	0.2513	0.0557	0.2442	-0.0554	-0.0361	0.1505	0.4279	0.0506	-0.1349	0.214	0.0325	0.2356	-21.5529	10.3883	-33.5694
20	6.3326	-0.5334	1.4239	3.1784	-0.4764	3.6275	-0.2263	0.0879	0.3296	0.5962	0.3007	0.231	-0.4686	0.2008	-0.1179	0.4811	-0.0848	-0.0073	0.2123	0.0847	0.3373	-20.7755	8.3581	-31.1476
21	2.3432	-0.9744	-0.1062	1.8076	-0.1113	3.1289	-0.109	0.4379	-0.4523	0.0653	0.1859	0.4452	-0.0606	-0.7569	-0.3348	0.219	-0.0198	-0.1349	0.2256	0.2261	0.3861	-30.3443	2.6078	-36.2889
22	0.8249	-0.0698	0.506	1.0686	0.2339	1.2651	-0.1701	-0.122	0.4827	0.0194	-0.0577	0.5849	-0.8292	-0.3357	0.1492	0.5268	0.0778	-0.0731	0.2095	0.0729	0.3421	-28.8997	13.9661	-36.8684

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 15 )
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 2 through 25 )
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 26 through 75 )
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 76 through 119 )
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 120 through 143 )
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 144 through 157 )
7	X-RAY DIFFRACTION	7	chain 'H' and (resid 158 through 177 )
8	X-RAY DIFFRACTION	8	chain 'H' and (resid 178 through 193 )
9	X-RAY DIFFRACTION	9	chain 'H' and (resid 194 through 213 )
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 2 through 18 )
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 19 through 27C)
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 28 through 48 )
13	X-RAY DIFFRACTION	13	chain 'L' and (resid 49 through 61 )
14	X-RAY DIFFRACTION	14	chain 'L' and (resid 62 through 75 )
15	X-RAY DIFFRACTION	15	chain 'L' and (resid 76 through 91 )
16	X-RAY DIFFRACTION	16	chain 'L' and (resid 92 through 101 )
17	X-RAY DIFFRACTION	17	chain 'L' and (resid 102 through 114 )
18	X-RAY DIFFRACTION	18	chain 'L' and (resid 115 through 130 )
19	X-RAY DIFFRACTION	19	chain 'L' and (resid 131 through 151 )
20	X-RAY DIFFRACTION	20	chain 'L' and (resid 152 through 172 )
21	X-RAY DIFFRACTION	21	chain 'L' and (resid 173 through 188 )
22	X-RAY DIFFRACTION	22	chain 'L' and (resid 189 through 209 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi