PDB-8p6i: Crystal structure of the 139H2 Fab fragment bound to Muc1 peptide...

ID or keywords:

Entry

Database: PDB / ID: 8p6i

Title

Crystal structure of the 139H2 Fab fragment bound to Muc1 peptide epitope

Components

139H2 HC
139H2 LC
Mucin-1

Keywords

IMMUNE SYSTEM / Fab fragment / peptide complex

Function / homology

Function and homology information

Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / negative regulation of cell adhesion mediated by integrin / negative regulation of transcription by competitive promoter binding / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Dectin-2 family / DNA damage response, signal transduction by p53 class mediator ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Beugelink, J.W. / Peng, W. / Siborova, M. / Pronker, M.F. / Snijder, J. / Janssen, B.J.C.

Funding support

Netherlands, 1items

Citation

Journal: Life Sci Alliance / Year: 2024
Title: Reverse-engineering the anti-MUC1 antibody 139H2 by mass spectrometry-based de novo sequencing.
Authors: Peng, W. / Giesbers, K.C. / Siborova, M. / Beugelink, J.W. / Pronker, M.F. / Schulte, D. / Hilkens, J. / Janssen, B.J. / Strijbis, K. / Snijder, J.

History

Deposition	May 26, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 3, 2024	Provider: repository / Type: Initial release
Revision 1.1	Apr 10, 2024	Group: Refinement description / Category: struct_ncs_dom / struct_ncs_dom_lim Item: _struct_ncs_dom.details / _struct_ncs_dom_lim.beg_auth_asym_id ..._struct_ncs_dom.details / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8p6i.cif.gz	448.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8p6i.ent.gz	283 KB	Display	PDB format
PDBx/mmJSON format	8p6i.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8p6i_validation.pdf.gz	433.8 KB	Display	wwPDB validaton report
Full document	8p6i_full_validation.pdf.gz	435 KB	Display
Data in XML	8p6i_validation.xml.gz	31.1 KB	Display
Data in CIF	8p6i_validation.cif.gz	44.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p6/8p6i ftp://data.pdbj.org/pub/pdb/validation_reports/p6/8p6i	HTTPS FTP

-
Related structure data

Similar structure data	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	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #169 - Jan 2014 HIV Envelope Glycoprotein similarity (1) #252 - Dec 2020 Hepatitis C Virus Protease/Helicase similarity (1) #62 - Feb 2005 Major Histocompatibility Complex similarity (1)

Deposited unit

A: Mucin-1

H: 139H2 HC

L: 139H2 LC

a: Mucin-1

h: 139H2 HC

l: 139H2 LC

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

1

A: Mucin-1

H: 139H2 HC

L: 139H2 LC

defined by author&software
Evidence: surface plasmon resonance
50.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

a: Mucin-1

h: 139H2 HC

l: 139H2 LC

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

Unit cell

Length a, b, c (Å)	211.833, 42.757, 129.064
Angle α, β, γ (deg.)	90.000, 122.306, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	H
2	1	h
3	2	L
4	2	l

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	GLN	GLN	ARG	ARG	H	B	1 - 222	1 - 222
2	1	1	GLN	GLN	ARG	ARG	h	E	1 - 222	1 - 222
3	2	2	ASP	ASP	GLU	GLU	L	C	1 - 219	1 - 219
4	2	2	ASP	ASP	GLU	GLU	l	F	1 - 219	1 - 219

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4

#1: Protein/peptide	Mucin-1 / MUC1-beta / MUC1-CT Mass: 881.952 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P15941
#2: Antibody	139H2 HC Mass: 25493.350 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Antibody	139H2 LC Mass: 24439.100 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.56 Å³/Da / Density % sol: 51.93 % / Description: long thin needles (<10 um diameter)
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: 0.2M NaCl 20%w/v PEG 8K 0.1M Na Phos Cit pH 4.2

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.6199 Å
Detector	Type: DECTRIS EIGER2 X CdTe 9M / Detector: PIXEL / Date: Mar 18, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.6199 Å / Relative weight: 1
Reflection	Resolution: 2.5→56.117 Å / Num. obs: 34554 / % possible obs: 100 % / Redundancy: 18.2 % / CC_1/2: 0.988 / R_merge(I) obs: 0.387 / R_pim(I) all: 0.093 / R_rim(I) all: 0.399 / Net I/σ(I): 9
Reflection shell	Resolution: 2.5→2.6 Å / Redundancy: 15.3 % / R_merge(I) obs: 1.813 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 3836 / CC_1/2: 0.689 / R_pim(I) all: 0.478 / R_rim(I) all: 1.876 / % possible all: 100

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0405	refinement
xia2.multiplex		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.5→56.117 Å / Cor.coef. F_o:F_c: 0.931 / Cor.coef. F_o:F_c free: 0.879 / WR_factor R_free: 0.201 / WR_factor R_work: 0.151 / SU B: 28.467 / SU ML: 0.286 / Average fsc free: 0.9477 / Average fsc work: 0.959 / Cross valid method: FREE R-VALUE / ESU R: 0.609 / ESU R Free: 0.297
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2538	1758	5.088 %
R_work	0.2031	32796	-
all	0.206	-	-
obs	-	34554	99.945 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 32.858 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.556 Å²	0 Å²	0.246 Å²
2-	-	-0.684 Å²	-0 Å²
3-	-	-	-0.102 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→56.117 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6719	0	0	229	6948

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.011	6888
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	6253
X-RAY DIFFRACTION	r_angle_refined_deg	1.325	1.654	9382
X-RAY DIFFRACTION	r_angle_other_deg	0.441	1.563	14494
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.008	5	864
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.414	5	24
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.104	10	1099
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.966	10	272
X-RAY DIFFRACTION	r_chiral_restr	0.059	0.2	1050
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	7921
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1543
X-RAY DIFFRACTION	r_nbd_refined	0.195	0.2	1013
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.201	0.2	5435
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	3292
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.089	0.2	3581
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.162	0.2	199
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.073	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.184	0.2	5
X-RAY DIFFRACTION	r_nbd_other	0.191	0.2	59
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.242	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	1.429	2.006	3486
X-RAY DIFFRACTION	r_mcbond_other	1.429	2.006	3486
X-RAY DIFFRACTION	r_mcangle_it	2.459	3.594	4340
X-RAY DIFFRACTION	r_mcangle_other	2.459	3.594	4341
X-RAY DIFFRACTION	r_scbond_it	1.709	2.165	3402
X-RAY DIFFRACTION	r_scbond_other	1.708	2.165	3401
X-RAY DIFFRACTION	r_scangle_it	2.884	3.886	5042
X-RAY DIFFRACTION	r_scangle_other	2.884	3.886	5043
X-RAY DIFFRACTION	r_lrange_it	4.202	18.569	7208
X-RAY DIFFRACTION	r_lrange_other	4.181	18.576	7193
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.097	0.05	6019
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.08	0.05	6701

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.09731	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.09731	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.07998	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.07998	0.0501

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.5-2.565	0.388	126	0.358	2393	0.36	2522	0.886	0.893	99.8811	0.358
2.565-2.635	0.325	126	0.344	2335	0.343	2461	0.91	0.907	100	0.343
2.635-2.711	0.354	109	0.35	2262	0.35	2371	0.887	0.905	100	0.349
2.711-2.794	0.356	99	0.306	2222	0.308	2321	0.926	0.93	100	0.303
2.794-2.886	0.31	108	0.255	2149	0.258	2257	0.937	0.955	100	0.248
2.886-2.987	0.268	109	0.227	2069	0.229	2178	0.958	0.965	100	0.212
2.987-3.099	0.246	112	0.204	2023	0.206	2135	0.962	0.972	100	0.185
3.099-3.225	0.232	120	0.192	1905	0.195	2025	0.961	0.977	100	0.166
3.225-3.368	0.208	95	0.183	1850	0.184	1945	0.972	0.982	100	0.16
3.368-3.532	0.236	101	0.181	1774	0.184	1875	0.966	0.984	100	0.163
3.532-3.722	0.255	94	0.178	1677	0.182	1771	0.956	0.984	100	0.161
3.722-3.947	0.251	84	0.175	1606	0.178	1690	0.962	0.984	100	0.155
3.947-4.218	0.218	90	0.166	1514	0.168	1604	0.969	0.985	100	0.139
4.218-4.554	0.191	80	0.133	1407	0.136	1487	0.978	0.99	100	0.111
4.554-4.985	0.244	86	0.132	1285	0.138	1371	0.97	0.99	100	0.103
4.985-5.568	0.215	60	0.142	1198	0.145	1258	0.982	0.991	100	0.111
5.568-6.419	0.275	59	0.182	1048	0.187	1107	0.962	0.985	100	0.14
6.419-7.836	0.225	50	0.188	908	0.19	958	0.971	0.983	100	0.143
7.836-10.975	0.169	31	0.146	735	0.147	766	0.983	0.988	100	0.116
10.975-56.117	0.237	19	0.245	436	0.245	458	0.972	0.964	99.345	0.207

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	8.7297	-1.964	5.2808	0.4436	-1.1871	3.1951	-0.0694	0.0893	0.2392	0.0158	-0.0522	-0.0559	-0.0203	0.0494	0.1216	0.0916	-0.0339	0.0429	0.0349	0.0056	0.045	-26.4613	17.174	-25.8068
2	0.7616	0.2927	-0.5868	0.9513	-1.4447	3.3713	-0.0039	-0.2043	-0.1132	0.0682	-0.0685	-0.068	0.1941	0.3101	0.0724	0.0845	0.0479	-0.018	0.1104	-0.0014	0.0387	-28.2595	-4.0326	-1.696
3	0.2641	-0.2487	0.0761	1.2414	-1.5389	2.4303	-0.0917	-0.1708	0.0295	0.2929	0.1146	-0.0674	-0.271	-0.0568	-0.0229	0.0934	0.0343	-0.0409	0.1289	-0	0.0318	-37.1269	8.8583	7.9602
4	2.9749	0.2714	3.4549	8.2621	2.6303	4.7264	-0.156	0.2728	-0.2415	-0.1494	0.2912	0.0941	-0.3335	0.2527	-0.1353	0.0921	0.1194	-0.0667	0.2899	-0.1668	0.1058	-0.5057	8.1654	78.7201
5	0.75	-0.2689	0.8266	1.0632	-1.552	3.777	-0.0397	0.0522	0.0909	0.0462	0.0363	0.1086	-0.1941	-0.2929	0.0034	0.08	0.0448	-0.0477	0.1483	-0.0517	0.0974	-11.5736	16.1407	49.7368
6	0.432	-0.2483	0.1963	0.2192	-0.5579	2.9837	0.0307	0.117	0.0336	-0.0468	-0.0772	-0.0104	0.071	0.0704	0.0466	0.0651	0.0027	-0.0344	0.1086	0.003	0.0268	4.8035	11.0707	42.9161

Refinement TLS group

Selection: ALL

-
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://pdbjlvh1.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