[English] 日本語
Yorodumi
- PDB-6cxl: anti-HIV-1 Fab 2G12 in complex with glycopeptide 10F5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6cxl
Titleanti-HIV-1 Fab 2G12 in complex with glycopeptide 10F5
Components
  • anti-HIV-1 Fab 2G12 heavy chain
  • anti-HIV-1 Fab 2G12 light chain
KeywordsIMMUNE SYSTEM / antibody / glycopeptide / HIV-1 / glycobiology
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.586 Å
AuthorsStanfield, R.L. / Wilson, I.A.
CitationJournal: ACS Cent Sci / Year: 2019
Title: Oligomannose Glycopeptide Conjugates Elicit Antibodies Targeting the Glycan Core Rather than Its Extremities.
Authors: Nguyen, D.N. / Xu, B. / Stanfield, R.L. / Bailey, J.K. / Horiya, S. / Temme, J.S. / Leon, D.R. / LaBranche, C.C. / Montefiori, D.C. / Costello, C.E. / Wilson, I.A. / Krauss, I.J.
History
DepositionApr 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: anti-HIV-1 Fab 2G12 light chain
H: anti-HIV-1 Fab 2G12 heavy chain
K: anti-HIV-1 Fab 2G12 light chain
M: anti-HIV-1 Fab 2G12 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,0506
Polymers94,0954
Non-polymers2,9552
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14130 Å2
ΔGint5 kcal/mol
Surface area38530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.641, 146.308, 148.213
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

#1: Antibody anti-HIV-1 Fab 2G12 light chain


Mass: 23201.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293freestyle / Production host: Homo sapiens (human)
#2: Antibody anti-HIV-1 Fab 2G12 heavy chain


Mass: 23845.791 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293freestyle / Production host: Homo sapiens (human)
#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose


Type: oligosaccharide / Mass: 1477.282 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-3[DManpa1-2DManpa1-6]DManpa1-6]DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,9,8/[a1122h-1b_1-5][a1122h-1a_1-5]/1-2-2-2-2-2-2-2-2/a3-b1_a6-e1_b2-c1_c2-d1_e3-f1_e6-h1_f2-g1_h2-i1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
Sequence detailsCrystals for 6CXG were grown from a complex of Fab 2G12 and glycopeptide 10F5 ((XXX)SPHLPVLLSK(XXX) ...Crystals for 6CXG were grown from a complex of Fab 2G12 and glycopeptide 10F5 ((XXX)SPHLPVLLSK(XXX)VLNDGRRIVQ(XXX)SSELP(XXX)VRRSGSGSG(BUC)A) where XXX are homopropargylglycine residues covalently linked to Man9 glycans via a cyclohexyl group. authors only see electron density for only the carbohydrate portion of the glycopeptide.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.97 Å3/Da / Density % sol: 68.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2M lithium sulfate, 17.5% Peg400, 0.1M tris

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.586→46.808 Å / Num. obs: 17760 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Biso Wilson estimate: 81.6 Å2 / CC1/2: 0.92 / Rmerge(I) obs: 0.296 / Rpim(I) all: 0.142 / Rrim(I) all: 0.316 / Rsym value: 0.296 / Net I/σ(I): 5.8
Reflection shellResolution: 3.586→3.68 Å / Redundancy: 8.6 % / Rmerge(I) obs: 1 / Num. unique obs: 1170 / CC1/2: 0.72 / Rpim(I) all: 0.48 / Rrim(I) all: 1 / Rsym value: 1 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.586→46.808 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2483 927 5.23 %
Rwork0.2186 --
obs0.2201 17716 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.586→46.808 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6548 0 198 0 6746
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056952
X-RAY DIFFRACTIONf_angle_d1.0639494
X-RAY DIFFRACTIONf_dihedral_angle_d13.6594216
X-RAY DIFFRACTIONf_chiral_restr0.0551132
X-RAY DIFFRACTIONf_plane_restr0.0071167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5863-3.77530.37911320.33382274X-RAY DIFFRACTION95
3.7753-4.01170.33641350.29012365X-RAY DIFFRACTION99
4.0117-4.32120.25721390.22462373X-RAY DIFFRACTION100
4.3212-4.75570.23471290.19972385X-RAY DIFFRACTION99
4.7557-5.4430.18741260.18232423X-RAY DIFFRACTION100
5.443-6.85410.22991270.21072429X-RAY DIFFRACTION100
6.8541-46.81170.2131390.18622540X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 32.5056 Å / Origin y: 38.4494 Å / Origin z: 0.3556 Å
111213212223313233
T0.693 Å2-0.0347 Å20.0312 Å2-0.6508 Å20.0305 Å2--0.6743 Å2
L0.4747 °20.3156 °20.2073 °2-0.4481 °20.073 °2--1.0401 °2
S-0.0773 Å °0.0255 Å °-0.0514 Å °0.0348 Å °0.1219 Å °-0.0529 Å °-0.181 Å °0.1362 Å °-0.0315 Å °
Refinement TLS groupSelection details: all

+
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