PDB-4yo0: Crystal structure of monoclonal anti-human podoplanin antibody NZ...

ID or keywords:

Entry

Database: PDB / ID: 4yo0

Title

Crystal structure of monoclonal anti-human podoplanin antibody NZ-1 with bound PA peptide

Components

Heavy chain of antigen binding fragment, Fab
Light chain of antigen binding fragment, Fab
PA14 peptide

Keywords

IMMUNE SYSTEM / Antibodies / Monoclonal / Antibody Affinity / Chromatography / Affinity / Epitopes / Rats / Immunoglobulin Fab Fragments / Kinetics / Peptides / Protein Binding / Proteins / Recombinant Fusion Proteins / Human podoplanin

Function / homology

Function and homology information

regulation of myofibroblast contraction / lymphatic endothelial cell fate commitment / actin-mediated cell contraction / leading edge of lamellipodium / regulation of substrate adhesion-dependent cell spreading / chemokine binding / Specification of primordial germ cells / positive regulation of extracellular matrix disassembly / lymphangiogenesis / regulation of lamellipodium morphogenesis ...
Similarity search - Function

Biological species

Rattus norvegicus (Norway rat)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.56 Å

Authors

Fujii, Y. / Kitago, Y. / Arimori, T. / Takagi, J.

Citation

Journal: J.Cell.Sci. / Year: 2016
Title: Tailored placement of a turn-forming PA tag into the structured domain of a protein to probe its conformational state
Authors: Fujii, Y. / Matsunaga, Y. / Arimori, T. / Kitago, Y. / Ogasawara, S. / Kaneko, M.K. / Kato, Y. / Takagi, J.

History

Deposition	Mar 11, 2015	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Mar 2, 2016	Provider: repository / Type: Initial release
Revision 1.1	Apr 13, 2016	Group: Database references
Revision 2.0	Feb 5, 2020	Group: Data collection / Derived calculations / Polymer sequence Category: diffrn_source / entity_poly / pdbx_struct_oper_list Item: _diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_oper_list.symmetry_operation
Revision 2.1	Nov 8, 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 / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4yo0.cif.gz	354.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4yo0.ent.gz	289.2 KB	Display	PDB format
PDBx/mmJSON format	4yo0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4yo0_validation.pdf.gz	488.3 KB	Display	wwPDB validaton report
Full document	4yo0_full_validation.pdf.gz	502.2 KB	Display
Data in XML	4yo0_validation.xml.gz	38 KB	Display
Data in CIF	4yo0_validation.cif.gz	55 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yo/4yo0 ftp://data.pdbj.org/pub/pdb/validation_reports/yo/4yo0	HTTPS FTP

-
Related structure data

Related structure data	4ynySC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5cd3-2 4qhk-1 3idi-d 4trp-d 5kg9-2 1r24-3 6p60-4 4qhk-2 5f6h-2 6y1m-d 5wca-d 5itb-d 4rnr-2 5ggu-2 7kqy-2 4ktd-d 4a6y-2 6nfn-1 3mme-3 6meg-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

4ynySC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (2) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (2) #245 - May 2020 Spliceosomes similarity (1) #148 - Apr 2012 Ras Protein similarity (1)

Deposited unit

A: Heavy chain of antigen binding fragment, Fab

B: Light chain of antigen binding fragment, Fab

C: Heavy chain of antigen binding fragment, Fab

D: Light chain of antigen binding fragment, Fab

E: PA14 peptide

F: PA14 peptide

hetero molecules

105 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Heavy chain of antigen binding fragment, Fab

B: Light chain of antigen binding fragment, Fab

E: PA14 peptide

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

2

C: Heavy chain of antigen binding fragment, Fab

D: Light chain of antigen binding fragment, Fab

F: PA14 peptide

hetero molecules

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

Unit cell

Length a, b, c (Å)	42.180, 80.010, 132.520
Angle α, β, γ (deg.)	90.00, 96.61, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Antibody	Heavy chain of antigen binding fragment, Fab Mass: 25560.020 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Mus musculus (house mouse)
#2: Antibody	Light chain of antigen binding fragment, Fab Mass: 25494.350 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Mus musculus (house mouse)
#3: Protein/peptide	PA14 peptide Mass: 1345.432 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q86YL7*PLUS
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 499 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Sequence details	THE SEQUENCES OF THIS PROTEIN WERE NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) ...THE SEQUENCES OF THIS PROTEIN WERE NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.11 Å³/Da / Density % sol: 41.59 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, sodium citrate

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 20, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 1.56→40 Å / Num. obs: 121358 / % possible obs: 97.2 % / Redundancy: 7.5 % / R_sym value: 0.057 / Net I/σ(I): 17.5
Reflection shell	Resolution: 1.56→1.65 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 1.5 / % possible all: 90.2

-
Processing

Software

Name	Version	Classification
PHENIX	(1.10_2155: 000)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4YNY

4yny

Resolution: 1.56→40 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.67

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2141	6035	4.98 %	RANDOM
R_work	0.1791	-	-	-
obs	0.1808	121132	97.47 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.56→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6441	0	4	499	6944

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.018	6755
X-RAY DIFFRACTION	f_angle_d	1.504	9230
X-RAY DIFFRACTION	f_dihedral_angle_d	15.044	4072
X-RAY DIFFRACTION	f_chiral_restr	0.1	1048
X-RAY DIFFRACTION	f_plane_restr	0.011	1185

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 (%)
1.56-1.5777	0.4321	166	0.3812	3118	X-RAY DIFFRACTION	81
1.5777-1.5963	0.3368	183	0.3214	3550	X-RAY DIFFRACTION	90
1.5963-1.6158	0.318	173	0.3036	3839	X-RAY DIFFRACTION	97
1.6158-1.6362	0.3209	217	0.2908	3791	X-RAY DIFFRACTION	97
1.6362-1.6577	0.2905	204	0.271	3770	X-RAY DIFFRACTION	97
1.6577-1.6804	0.3068	191	0.2625	3864	X-RAY DIFFRACTION	97
1.6804-1.7045	0.2859	200	0.2435	3832	X-RAY DIFFRACTION	98
1.7045-1.7299	0.2796	198	0.2416	3778	X-RAY DIFFRACTION	97
1.7299-1.7569	0.2584	204	0.2339	3889	X-RAY DIFFRACTION	98
1.7569-1.7857	0.2371	197	0.2136	3753	X-RAY DIFFRACTION	97
1.7857-1.8165	0.2602	207	0.2066	3888	X-RAY DIFFRACTION	98
1.8165-1.8496	0.2279	203	0.2034	3829	X-RAY DIFFRACTION	98
1.8496-1.8851	0.2321	202	0.1952	3835	X-RAY DIFFRACTION	98
1.8851-1.9236	0.2397	206	0.1908	3899	X-RAY DIFFRACTION	98
1.9236-1.9654	0.246	201	0.1912	3836	X-RAY DIFFRACTION	98
1.9654-2.0112	0.2299	206	0.1903	3914	X-RAY DIFFRACTION	98
2.0112-2.0614	0.216	199	0.1909	3809	X-RAY DIFFRACTION	99
2.0614-2.1172	0.2544	205	0.1866	3903	X-RAY DIFFRACTION	99
2.1172-2.1795	0.2375	204	0.1824	3852	X-RAY DIFFRACTION	99
2.1795-2.2498	0.2185	205	0.1812	3903	X-RAY DIFFRACTION	99
2.2498-2.3302	0.2295	204	0.1861	3924	X-RAY DIFFRACTION	99
2.3302-2.4235	0.1952	206	0.1923	3893	X-RAY DIFFRACTION	99
2.4235-2.5338	0.2401	206	0.1917	3909	X-RAY DIFFRACTION	99
2.5338-2.6673	0.2411	208	0.1897	3945	X-RAY DIFFRACTION	99
2.6673-2.8344	0.2058	206	0.1836	3926	X-RAY DIFFRACTION	99
2.8344-3.0532	0.2326	207	0.1841	3926	X-RAY DIFFRACTION	100
3.0532-3.3603	0.2036	207	0.1812	3933	X-RAY DIFFRACTION	100
3.3603-3.8462	0.1844	209	0.1549	3973	X-RAY DIFFRACTION	100
3.8462-4.8445	0.1756	209	0.1295	3961	X-RAY DIFFRACTION	100
4.8445-40.0181	0.1697	202	0.1543	3855	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	3.403	-0.1427	1.6553	2.1949	-0.0417	2.175	-0.1705	-0.3238	-0.1204	0.0833	0.1672	0.1207	-0.1105	-0.1226	0.0059	0.183	0.0212	0.049	0.1763	0.0368	0.1862	-52.7074	13.2613	-55.4384
2	3.5902	-0.8042	-0.6183	3.9045	0.053	6.4216	-0.0769	-0.1534	-0.1297	0.2986	0.0814	0.0252	0.6283	-0.1531	-0.0163	0.4895	0.0222	-0.0057	0.2797	0.0156	0.1952	-44.0353	33.8134	-33.2712
3	1.463	-0.6438	-0.1161	7.0448	0.6889	1.2317	-0.026	-0.047	0.0029	0.0551	0.1015	0.4043	0.0621	-0.0984	-0.0672	0.2319	0.0073	-0.0053	0.1746	0.0305	0.1966	-63.3596	31.7487	-64.2808
4	4.1806	-1.4798	2.3826	5.0509	-1.2619	6.5366	-0.2458	-0.0783	0.2963	0.2304	-0.0629	-0.6928	-0.7508	0.342	0.295	0.527	-0.0436	-0.037	0.2928	0.0667	0.2902	-39.5939	48.0531	-40.8213
5	1.8699	1.6135	0.4259	4.2881	1.788	3.2186	-0.3017	0.2076	0.275	-0.645	0.2336	0.3051	-0.2898	-0.0206	0.0141	0.2542	-0.0174	-0.0455	0.1643	0.0299	0.2832	-27.6198	25.815	-8.6946
6	4.3853	-0.2717	0.8446	4.77	-0.1601	5.1346	0.1889	-0.1721	-0.4156	-0.9538	0.302	0.9421	-0.5133	-0.5107	-0.4083	0.5822	0.0124	-0.1271	0.3501	0.1222	0.4614	-38.111	7.3409	-28.4102
7	2.0218	0.6811	0.0427	6.4893	0.894	0.6703	-0.0112	-0.1848	-0.0152	0.5424	0.0465	-0.1479	0.006	-0.055	-0.0297	0.2255	0.0144	-0.0085	0.1621	0.0132	0.1872	-27.2623	7.4964	5.0722
8	2.8527	0.1789	2.6884	2.8905	-0.3731	5.5844	0.3024	0.0654	-0.5689	-0.9457	0.3893	0.4281	0.2857	-0.2282	-0.6268	0.5985	-0.0285	-0.2051	0.3444	0.0651	0.5088	-30.6634	-7.6868	-28.7994
9	7.4865	3.7129	-5.2744	5.8428	-2.4209	8.2401	-0.0664	0.2241	-0.561	-0.3695	0.018	0.8842	-0.1598	-0.9844	0.0763	0.2229	0.0129	-0.0545	0.2351	0.017	0.4387	-67.2766	10.9532	-64.9584
10	4.8024	-4.5642	0.3299	4.9107	0.9376	2.7246	-0.201	-0.5478	0.3517	0.9364	-0.0093	0.2664	0.0722	-0.5317	0.2053	0.3277	0.0148	0.0207	0.2265	-0.0468	0.3522	-29.2723	28.9482	7.9986

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resseq 20:137)
2	X-RAY DIFFRACTION	2	(chain A and resseq 138:235)
3	X-RAY DIFFRACTION	3	(chain B and resseq 20:130)
4	X-RAY DIFFRACTION	4	(chain B and resseq 131:229)
5	X-RAY DIFFRACTION	5	(chain C and resseq 20:137)
6	X-RAY DIFFRACTION	6	(chain C and resseq 138:235)
7	X-RAY DIFFRACTION	7	(chain D and resseq 20:130)
8	X-RAY DIFFRACTION	8	(chain D and resseq 131:229)
9	X-RAY DIFFRACTION	9	(chain E and resseq 3:14)
10	X-RAY DIFFRACTION	10	(chain F and resseq 4:14)

-
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