[English] 日本語
Yorodumi
- PDB-6uud: Crystal structure of antibody 5D5 in complex with PfCSP N-termina... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6uud
TitleCrystal structure of antibody 5D5 in complex with PfCSP N-terminal peptide
Components
  • (5D5 Antibody Fab, ...) x 2
  • Circumsporozoite protein
KeywordsIMMUNE SYSTEM / Malaria / Antibody
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
Plasmodium circumsporozoite protein / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat
Similarity search - Domain/homology
Circumsporozoite protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsThai, E. / Scally, S.W. / Julien, J.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1179906; J.-P.J. United States
CitationJournal: J.Exp.Med. / Year: 2020
Title: A high-affinity antibody against the CSP N-terminal domain lacks Plasmodium falciparum inhibitory activity.
Authors: Thai, E. / Costa, G. / Weyrich, A. / Murugan, R. / Oyen, D. / Flores-Garcia, Y. / Prieto, K. / Bosch, A. / Valleriani, A. / Wu, N.C. / Pholcharee, T. / Scally, S.W. / Wilson, I.A. / ...Authors: Thai, E. / Costa, G. / Weyrich, A. / Murugan, R. / Oyen, D. / Flores-Garcia, Y. / Prieto, K. / Bosch, A. / Valleriani, A. / Wu, N.C. / Pholcharee, T. / Scally, S.W. / Wilson, I.A. / Wardemann, H. / Julien, J.P. / Levashina, E.A.
History
DepositionOct 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 27, 2021Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Apr 3, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: 5D5 Antibody Fab, heavy chain
L: 5D5 Antibody Fab, light chain
A: Circumsporozoite protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9285
Polymers49,2953
Non-polymers6332
Water7,494416
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-3 kcal/mol
Surface area19650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.601, 60.901, 72.435
Angle α, β, γ (deg.)90.000, 97.666, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

-
Antibody , 2 types, 2 molecules HL

#1: Antibody 5D5 Antibody Fab, heavy chain


Mass: 23468.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody 5D5 Antibody Fab, light chain


Mass: 23631.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)

-
Protein/peptide / Sugars , 2 types, 2 molecules A

#3: Protein/peptide Circumsporozoite protein


Mass: 2195.604 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: P02893*PLUS
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

-
Non-polymers , 2 types, 417 molecules

#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.27 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG 3350, 0.2 M di-ammonium citrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97959 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97959 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. obs: 38412 / % possible obs: 98.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 25.42 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.7
Reflection shellResolution: 1.85→1.95 Å / Num. unique obs: 5588 / CC1/2: 0.74

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: internal

Resolution: 1.85→39.74 Å / SU ML: 0.2324 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.1855
RfactorNum. reflection% reflection
Rfree0.2235 1920 5 %
Rwork0.1781 --
obs0.1804 38396 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 33.1 Å2
Refinement stepCycle: LAST / Resolution: 1.85→39.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3391 0 42 416 3849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00543534
X-RAY DIFFRACTIONf_angle_d0.79134809
X-RAY DIFFRACTIONf_chiral_restr0.0529549
X-RAY DIFFRACTIONf_plane_restr0.005609
X-RAY DIFFRACTIONf_dihedral_angle_d13.34542126
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.32511370.27612606X-RAY DIFFRACTION98.78
1.9-1.950.29411350.23792577X-RAY DIFFRACTION98.69
1.95-20.28241350.21712562X-RAY DIFFRACTION98.32
2-2.070.27941380.22042596X-RAY DIFFRACTION98.17
2.07-2.140.29791350.21612560X-RAY DIFFRACTION98.43
2.14-2.230.26011340.21272569X-RAY DIFFRACTION98.04
2.23-2.330.31951370.20342603X-RAY DIFFRACTION98.42
2.33-2.450.24971380.20382609X-RAY DIFFRACTION98.99
2.45-2.610.24641360.20642582X-RAY DIFFRACTION98.26
2.61-2.810.24831370.19852610X-RAY DIFFRACTION98.81
2.81-3.090.22711380.18012626X-RAY DIFFRACTION99.28
3.09-3.540.20021390.1592631X-RAY DIFFRACTION99.28
3.54-4.460.15931390.13862646X-RAY DIFFRACTION99.11
4.46-39.740.19081420.14692699X-RAY DIFFRACTION99.37
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)
13.08456076787-2.299201573812.476406923894.63408830023-3.592646057715.165978088430.00637556311745-0.327820825993-0.249941580376-0.0591791586710.2618011633750.2482726438380.393886654715-0.0549921665787-0.2883976264390.2818315405030.01551278707960.0753057552920.2307747186060.02445186093610.211365482679-22.7447009659-14.5023058869-6.48423418872
28.01193231322-1.09015617410.2549331252678.6538542456-1.133815371954.868434410770.01312514531020.3982893053280.0400823745074-0.06261736974620.315515657244-0.132784894056-0.4212034550610.384289258197-0.2142265533090.184201736502-0.01907074595640.02113133469180.263607505334-0.04459022261050.161357366131-13.5690719658-6.98932892672-7.98168255389
33.03445819803-1.012599007341.61097739161.11562457486-0.7116166915775.23024225743-0.22400556752-0.4698180308130.165206589430.4904248000570.3737492910040.16191240267-0.6189181992670.0116391684566-0.02259135459510.319992146150.04987687537460.05269243508610.272702384671-0.05024135902570.208243790369-20.5661516402-5.33746924757-1.52763293932
42.96864886254-0.3324110794471.035979405052.44607148131-0.2964599006815.390694037230.0556727767884-0.104385149632-0.3100020214790.1955354596990.13702008124-0.09739463884520.3705335352420.827752760341-0.1864956905590.3023763206660.07971612414480.01854740068930.337275750543-0.0227886511340.205699983082-11.8195554461-14.8015027615-7.35956310605
51.07923731882-0.360190347001-0.4888062457553.676738653421.671776726861.738324420540.02473107317040.0317776525473-0.0440226659382-0.0813023609419-0.03409648322530.126890346652-0.0573239558102-0.1656322203340.007843639695540.1501163293340.01812570897440.008101793708660.1465142921070.02555053924490.160364908392-27.5292922245-18.0190333327-32.5401991134
61.857277820370.6513220143081.16737673752.484626441930.1554149809460.771534772441-0.02231313906970.121774780186-0.3280528429830.1385472973760.08896669125280.4685666800210.331703864949-0.320112967485-0.03666111846930.237892291382-0.03387189259930.0138024622090.256581529167-0.0002194587424140.355089439309-35.0462072629-24.1544440853-32.8541738256
73.31431149228-0.9718845201880.2244030527575.691320092393.560734592916.898454640160.033866133822-0.2639946509420.4167930509960.08513331645280.0241845862604-0.523700567056-0.4170912675520.795229976202-0.04673027740040.231894463886-0.1166830485010.03656254875320.376071774339-0.00948573826390.2952653903953.79468234691-7.62451704838-21.5618834678
83.079130528760.02753333796750.6950240363193.106552038891.772171511965.22104901822-0.0979431576493-0.5711986110730.00708499408550.3189444446350.0903520227606-0.2432036056640.1990473651580.579771791001-0.008057227437830.1942843770650.004222278893780.006908734443680.3992603146080.02093993704790.1902875814630.564502162132-13.9730023444-14.0409094549
90.4450308317741.3574249141.938034974983.814384590345.313528931878.52334763217-0.09576978484570.1252524294830.00752573168253-0.117957735880.0996053533926-0.117912684115-0.0265487579430.5263679800670.002626924705350.1860654414880.03536085767250.02832865023850.219142732403-0.02455113003710.249151586291-3.55213031216-14.6656401453-36.8767065183
103.95515004132-0.768520377589-0.4442698859842.43853307133-0.2049901646722.59108165339-0.002218389445020.184847976754-0.157554675691-0.07029139105610.0237143843120.4045893877430.0752819939596-0.418724358549-0.05122713659260.209418053997-0.0133937572214-0.04122546865310.227934190808-0.009853018232730.23169985977-33.8261233228-16.8818426096-43.5668937414
115.76545763146-1.366907000820.2635162530872.2476240781-0.4287881838621.667980621330.001117413269280.07495234881470.271634759977-0.0860548806010.00727632928365-0.116689347269-0.07113780936190.120786240403-0.0002892867532280.2134045518050.0135102813024-0.009095634786950.170326277418-0.01354999849160.173103662476-19.1379510587-11.3636255221-45.3908398589
127.64987034304-4.340203631064.433984913893.7360026756-2.474821257685.06569655931-0.04835165490030.07985951824060.0171259068945-0.02989253286210.06974163959910.0530163007995-0.03302817822160.122442046037-0.06584490501880.157734284825-0.04704921573510.02863924992020.128223788994-0.02434023323430.192689173849-18.0057865309-11.163829591-41.6173884584
134.05402718678-0.516406376003-0.6768457097591.167017923460.3781369368352.304653312280.06786896016970.6792385253810.0995187878583-0.272852855816-0.03505029937290.1007719238230.0230156213266-0.357031267316-0.06616962534570.281092876287-0.00549443148113-0.01195635460690.2280115310010.04070462774480.185488206951-26.8706282227-11.8951593634-51.3476910884
148.668820754283.46683617384.332572467556.952951175624.782937311293.84584759141-0.179045268266-1.048505817730.1070813568480.5738669902030.304486977095-0.324355637943-0.500141842920.877496484417-0.09194176070130.4619579470010.03716066449230.002287352522580.719788338572-0.1021324829460.287617190614-5.71132358571-11.39253935786.66580380695
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 32 )
2X-RAY DIFFRACTION2chain 'H' and (resid 33 through 52 )
3X-RAY DIFFRACTION3chain 'H' and (resid 52A through 87 )
4X-RAY DIFFRACTION4chain 'H' and (resid 88 through 106 )
5X-RAY DIFFRACTION5chain 'H' and (resid 107 through 203 )
6X-RAY DIFFRACTION6chain 'H' and (resid 204 through 215 )
7X-RAY DIFFRACTION7chain 'L' and (resid 1 through 25 )
8X-RAY DIFFRACTION8chain 'L' and (resid 26 through 101 )
9X-RAY DIFFRACTION9chain 'L' and (resid 102 through 113 )
10X-RAY DIFFRACTION10chain 'L' and (resid 114 through 128 )
11X-RAY DIFFRACTION11chain 'L' and (resid 129 through 150 )
12X-RAY DIFFRACTION12chain 'L' and (resid 151 through 174 )
13X-RAY DIFFRACTION13chain 'L' and (resid 175 through 213 )
14X-RAY DIFFRACTION14chain 'A' and (resid 81 through 92 )

+
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://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

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