[English] 日本語
Yorodumi
- PDB-3tnm: Crystal structure of A32 Fab, an ADCC mediating anti-HIV-1 antibody -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tnm
TitleCrystal structure of A32 Fab, an ADCC mediating anti-HIV-1 antibody
Components
  • Fab heavy chain of human anti-HIV-1 Env antibody A32
  • Fab light chain of human anti-HIV-1 Env antibody A32
KeywordsIMMUNE SYSTEM / ADCC / NON-NEUTRALIZING / ANTI-HIV-1 ENV ANTIBODY A32 / CD4i antibody / Fab / VIRAL GLYCOPROTEIN GP120 / HIV-1 Env
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsWu, X. / Pazgier, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Diverse specificity and effector function among human antibodies to HIV-1 envelope glycoprotein epitopes exposed by CD4 binding.
Authors: Guan, Y. / Pazgier, M. / Sajadi, M.M. / Kamin-Lewis, R. / Al-Darmarki, S. / Flinko, R. / Lovo, E. / Wu, X. / Robinson, J.E. / Seaman, M.S. / Fouts, T.R. / Gallo, R.C. / DeVico, A.L. / Lewis, G.K.
History
DepositionSep 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Apr 21, 2021Group: Derived calculations / Source and taxonomy / Category: entity_src_gen / struct_site
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name ..._entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: Fab heavy chain of human anti-HIV-1 Env antibody A32
L: Fab light chain of human anti-HIV-1 Env antibody A32
A: Fab heavy chain of human anti-HIV-1 Env antibody A32
B: Fab light chain of human anti-HIV-1 Env antibody A32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,3578
Polymers95,1924
Non-polymers1654
Water6,377354
1
H: Fab heavy chain of human anti-HIV-1 Env antibody A32
L: Fab light chain of human anti-HIV-1 Env antibody A32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7265
Polymers47,5962
Non-polymers1303
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-24 kcal/mol
Surface area19080 Å2
MethodPISA
2
A: Fab heavy chain of human anti-HIV-1 Env antibody A32
B: Fab light chain of human anti-HIV-1 Env antibody A32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6313
Polymers47,5962
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-25 kcal/mol
Surface area18670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.780, 71.316, 77.673
Angle α, β, γ (deg.)103.69, 104.02, 105.40
Int Tables number1
Space group name H-MP1

-
Components

#1: Antibody Fab heavy chain of human anti-HIV-1 Env antibody A32


Mass: 24766.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#2: Antibody Fab light chain of human anti-HIV-1 Env antibody A32


Mass: 22829.080 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.47 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES sodium pH 7.5, 10% 2-Propanol, 20% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 297K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 59060 / % possible obs: 80 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.12 / Rsym value: 0.107 / Net I/σ(I): 20
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 1.5 / Num. unique all: 2898 / Rsym value: 0.903 / % possible all: 89.5

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 8.494 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23203 3000 5.1 %RANDOM
Rwork0.18728 ---
all0.18957 3942 --
obs0.18957 56011 89.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.123 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0.2 Å21.56 Å2
2---1.32 Å20.22 Å2
3---2.23 Å2
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6449 0 7 354 6810
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0226631
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.9499059
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7265853
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.66124.132242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.979151005
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3081522
X-RAY DIFFRACTIONr_chiral_restr0.1180.21027
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215002
X-RAY DIFFRACTIONr_mcbond_it2.3181.54278
X-RAY DIFFRACTIONr_mcangle_it4.01726941
X-RAY DIFFRACTIONr_scbond_it4.45432353
X-RAY DIFFRACTIONr_scangle_it7.2594.52118
LS refinement shellResolution: 1.853→1.901 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 198 -
Rwork0.26 3942 -
obs--86.99 %
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)
10.1906-0.3859-0.07190.80350.12060.16110.03130.0282-0.0007-0.035-0.06580.010.0183-0.01650.03450.08610.00610.00360.0789-0.00630.0822-14.508745.30846.7657
20.0395-0.15040.1051.0449-0.27010.40920.0333-0.0251-0.0053-0.1245-0.0313-0.00090.0029-0.1002-0.0020.09930.0176-0.00930.10330.01720.0181-15.452943.977730.516
30.24070.3387-0.0150.58430.14140.2511-0.0038-0.0194-0.0276-0.0006-0.0399-0.0240.0078-0.02330.04370.0651-0.0048-0.03470.09480.00440.09352.887125.361-6.0169
40.12280.0202-0.20660.8276-0.1240.3691-0.03160.03490.01690.07860.04350.03120.0275-0.0418-0.01190.0720.0081-0.04070.11650.02380.0385-0.50326.59379.7733
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 214
2X-RAY DIFFRACTION2L4 - 208
3X-RAY DIFFRACTION3A1 - 214
4X-RAY DIFFRACTION4B4 - 208

+
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