[English] 日本語
Yorodumi
- PDB-6hig: hPD-1/NBO1a Fab complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hig
TitlehPD-1/NBO1a Fab complex
Components
  • Heavy Chain
  • Light Chain
  • Programmed cell death protein 1
KeywordsIMMUNE SYSTEM / Non-blocking antibody / PD-1/PD-L1 pathway / anti-PD-1 antibody / tumor clearance
Function / homology
Function and homology information


negative regulation of immune response / negative regulation of T cell mediated immune response to tumor cell / negative regulation of T cell activation / humoral immune response / Co-inhibition by PD-1 / regulation of immune response / negative regulation of T cell receptor signaling pathway / PD-L1(CD274) glycosylation and translocation to plasma membrane / negative regulation of inflammatory response / transmembrane signaling receptor activity ...negative regulation of immune response / negative regulation of T cell mediated immune response to tumor cell / negative regulation of T cell activation / humoral immune response / Co-inhibition by PD-1 / regulation of immune response / negative regulation of T cell receptor signaling pathway / PD-L1(CD274) glycosylation and translocation to plasma membrane / negative regulation of inflammatory response / transmembrane signaling receptor activity / signaling receptor activity / Potential therapeutics for SARS / adaptive immune response / external side of plasma membrane / apoptotic process / plasma membrane
Similarity search - Function
Programmed cell death protein 1 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold ...Programmed cell death protein 1 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Programmed cell death protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLoredo-Varela, J.L. / Fenwick, C. / Pantaleo, G. / Weissenhorn, W.
CitationJournal: J.Exp.Med. / Year: 2019
Title: Tumor suppression of novel anti-PD-1 antibodies mediated through CD28 costimulatory pathway.
Authors: Fenwick, C. / Loredo-Varela, J.L. / Joo, V. / Pellaton, C. / Farina, A. / Rajah, N. / Esteves-Leuenberger, L. / Decaillon, T. / Suffiotti, M. / Noto, A. / Ohmiti, K. / Gottardo, R. / ...Authors: Fenwick, C. / Loredo-Varela, J.L. / Joo, V. / Pellaton, C. / Farina, A. / Rajah, N. / Esteves-Leuenberger, L. / Decaillon, T. / Suffiotti, M. / Noto, A. / Ohmiti, K. / Gottardo, R. / Weissenhorn, W. / Pantaleo, G.
History
DepositionAug 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 17, 2024Group: 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 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: Heavy Chain
L: Light Chain
B: Programmed cell death protein 1


Theoretical massNumber of molelcules
Total (without water)61,7323
Polymers61,7323
Non-polymers00
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-33 kcal/mol
Surface area22590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.514, 63.049, 68.297
Angle α, β, γ (deg.)90.00, 106.49, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Antibody Heavy Chain


Mass: 25238.256 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#2: Antibody Light Chain


Mass: 23264.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Protein Programmed cell death protein 1 / hPD-1


Mass: 13228.716 Da / Num. of mol.: 1 / Mutation: C93S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD1, PD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15116
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.98 %
Crystal growTemperature: 293 K / Method: evaporation / Details: 0.2 M NH4I 20 % PEG 3.35 K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.2→65.49 Å / Num. obs: 26237 / % possible obs: 97.59 % / Redundancy: 2.9 % / Biso Wilson estimate: 33.88 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.0696 / Rrim(I) all: 0.08456 / Net I/σ(I): 10.77
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.5201 / Mean I/σ(I) obs: 2.16 / Num. unique obs: 2261 / CC1/2: 0.711 / Rrim(I) all: 0.6447 / % possible all: 98.28

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZQK, 4Q9Q

4zqk

4q9q


Resolution: 2.2→65.489 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.83
RfactorNum. reflection% reflection
Rfree0.2697 1265 4.82 %
Rwork0.2148 --
obs0.2174 26236 97.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→65.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3787 0 0 155 3942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023875
X-RAY DIFFRACTIONf_angle_d0.4795270
X-RAY DIFFRACTIONf_dihedral_angle_d12.5272306
X-RAY DIFFRACTIONf_chiral_restr0.041603
X-RAY DIFFRACTIONf_plane_restr0.004665
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.28810.35941570.28392769X-RAY DIFFRACTION98
2.2881-2.39230.30971260.27222799X-RAY DIFFRACTION99
2.3923-2.51840.32951480.25682806X-RAY DIFFRACTION99
2.5184-2.67620.31131370.24862758X-RAY DIFFRACTION98
2.6762-2.88280.32761450.24192740X-RAY DIFFRACTION97
2.8828-3.17290.29761360.22782812X-RAY DIFFRACTION98
3.1729-3.6320.29421280.20572755X-RAY DIFFRACTION97
3.632-4.57580.21161360.17792786X-RAY DIFFRACTION97
4.5758-65.51760.22661520.19282746X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
13.0718-0.64660.07021.6787-0.49462.9325-0.06220.65210.4873-0.9381-0.31850.7166-0.7338-0.69570.40430.32930.1245-0.2750.4643-0.21350.6255-19.8813-11.4614-28.8662
22.0649-0.1462-2.05064.04781.4434.05170.21150.27710.181-0.7898-0.31930.2735-0.7408-0.07940.0830.61370.012-0.08020.4896-0.07020.2984-9.9823-17.2229-33.5151
35.1003-3.4407-5.45626.32925.46968.9583-0.1054-0.53850.06230.67670.03080.80180.2866-0.77520.21640.40480.04910.1350.5596-0.11120.3862-14.1152-23.4845-21.7579
44.6151.8797-6.40061.9269-2.94439.0206-0.16440.5714-1.2786-0.2389-1.13030.3722-0.2724-0.66350.86780.5453-0.080.02950.5306-0.25290.5881-13.1789-28.5119-34.4553
54.04712.9138-0.61224.8216-1.083.7102-0.27470.58640.8212-2.3782-0.59711.23960.1975-0.71630.1240.80020.0858-0.44720.4643-0.42880.7166-18.0701-20.1238-36.2322
64.05841.20340.35114.00791.5414.6738-0.21390.11680.3484-0.3328-0.30.4464-0.0816-0.3620.57910.41120.0216-0.04120.2903-0.07450.2607-12.7883-19.1925-26.555
75.9469-2.8475-0.99544.52361.97293.14610.2260.182-0.9354-0.4128-0.0310.2802-0.3711-0.0886-0.17310.41950.0472-0.09150.4161-0.14890.4104-29.6999-8.9038-19.4667
84.76851.52923.60138.7312.94077.5161-0.2417-0.11580.26980.1735-0.0156-0.07310.02820.09820.24040.2290.04420.02140.2468-0.01370.1782-27.40830.57610.7056
94.17720.7522.24733.98840.82374.74450.2020.14550.20610.1638-0.26760.06530.24690.09910.07820.18660.04290.0790.26550.02280.2127-21.7593-0.7168-5.0131
108.86332.66886.53618.8354.94865.6052-0.51150.25530.673-0.3063-0.13550.3516-0.99350.20710.73670.35870.0911-0.01840.23550.0360.3314-26.12137.8445-6.0156
113.1137-0.41890.24563.33190.97721.7845-0.0145-0.2985-0.3770.3509-0.12790.2580.2392-0.06810.16170.38380.0520.12280.2950.05210.2597-0.2473-25.5257-11.0169
122.62421.63060.56311.7759-1.09723.6766-0.16280.06720.0937-0.3928-0.0886-0.46870.05310.39150.23010.28770.070.05510.2775-0.02420.1974.3383-21.4368-17.7646
130.8196-1.4745-2.34622.14964.17417.8394-0.0567-0.1661-0.11650.1866-0.24550.0640.5122-0.02550.27040.2790.03650.02920.31970.03850.2066-2.701-18.4288-8.8097
148.17820.43955.45412.532-0.21267.6622-0.18230.44850.9534-0.1647-0.15660.3053-0.4935-0.49230.18770.26350.04170.01120.2656-0.02420.238-32.6811-1.42754.7719
152.7691-0.4534-0.24861.3336-0.21932.0075-0.29620.51350.2902-0.07280.0506-0.01550.4009-0.13480.35760.2831-0.00920.03490.2585-0.02120.2176-21.7594-11.72866.1029
169.80112.403-5.61262.1493-2.89594.974-0.17290.0999-0.069-0.0210.1583-0.0820.42460.03230.21420.4020.0335-0.00550.1725-0.05070.1987-29.734-16.11594.7314
174.9505-0.45070.52280.3392-0.22561.5769-0.0929-0.037-0.110.00290.09610.04130.0635-0.119-0.05990.29670.03280.01470.1653-0.00720.1964-24.7586-9.84317.8226
188.5246-0.2449-2.74845.8449-2.23432.35140.2956-0.0496-0.46560.0402-0.4496-0.5118-0.31960.14720.13860.45520.03350.0050.4520.01840.24647.7627-26.0644-41.6573
193.11982.8759-1.33669.5854-3.24115.6877-0.4604-0.4413-0.5022-0.72390.2774-0.57210.66770.38180.21910.40360.07560.050.58780.1580.445515.7396-24.8488-43.1937
205.19391.5627-0.93135.5928-1.05180.5154-0.2752-0.1087-0.1928-0.0035-0.0072-0.07590.27310.070.32360.46790.02670.02590.4660.00660.25019.9477-28.0449-39.8675
218.48460.45210.87214.19924.98825.9892-0.46510.7036-0.99170.36820.06440.79121.12460.7540.32430.5359-0.0320.02310.3824-0.10360.5541-0.4444-34.7081-44.5505
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 17 )
2X-RAY DIFFRACTION2chain 'H' and (resid 18 through 39 )
3X-RAY DIFFRACTION3chain 'H' and (resid 40 through 51 )
4X-RAY DIFFRACTION4chain 'H' and (resid 52 through 64 )
5X-RAY DIFFRACTION5chain 'H' and (resid 65 through 83 )
6X-RAY DIFFRACTION6chain 'H' and (resid 84 through 110 )
7X-RAY DIFFRACTION7chain 'H' and (resid 111 through 123 )
8X-RAY DIFFRACTION8chain 'H' and (resid 124 through 149 )
9X-RAY DIFFRACTION9chain 'H' and (resid 150 through 192 )
10X-RAY DIFFRACTION10chain 'H' and (resid 193 through 217 )
11X-RAY DIFFRACTION11chain 'L' and (resid 2 through 38 )
12X-RAY DIFFRACTION12chain 'L' and (resid 39 through 75 )
13X-RAY DIFFRACTION13chain 'L' and (resid 76 through 113 )
14X-RAY DIFFRACTION14chain 'L' and (resid 114 through 128 )
15X-RAY DIFFRACTION15chain 'L' and (resid 129 through 150 )
16X-RAY DIFFRACTION16chain 'L' and (resid 151 through 163 )
17X-RAY DIFFRACTION17chain 'L' and (resid 164 through 211 )
18X-RAY DIFFRACTION18chain 'B' and (resid 33 through 69 )
19X-RAY DIFFRACTION19chain 'B' and (resid 75 through 104 )
20X-RAY DIFFRACTION20chain 'B' and (resid 105 through 139 )
21X-RAY DIFFRACTION21chain 'B' and (resid 140 through 147 )

+
About Yorodumi

-
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

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

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

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more