Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 99.14 kDa 
• Atom Count: 7395 
• Residue Count: 865 
• Unique protein chains: 2

1RZG

Crystal structure of Human anti-HIV-1 GP120 reactive antibody 412d

• DOI: 10.2210/pdb1RZG/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Human gammaherpesvirus 4
• Mutation(s): No 


• Deposited: 2003-12-24 Released: 2004-02-03 
• Deposition Author(s): Huang, C.C., Venturi, M., Majeed, S., Moore, M.J., Phogat, S., Zhang, M.-Y., Dimitrov, D.S., Hendrickson, W.A., Robinson, J., Sodroski, J., Wyatt, R., Choe, H., Farzan, M., Kwong, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.251 
• R-Value Work: 0.201 
• R-Value Observed: 0.201 

Literature

Structural basis of tyrosine sulfation and VH-gene usage in antibodies that recognize the HIV type 1 coreceptor-binding site on gp120

Huang, C.C., Venturi, M., Majeed, S., Moore, M.J., Phogat, S., Zhang, M.-Y., Dimitrov, D.S., Hendrickson, W.A., Robinson, J., Sodroski, J., Wyatt, R., Choe, H., Farzan, M., Kwong, P.D.

(2004) Proc Natl Acad Sci U S A 101: 2706-2711

• PubMed: 14981267 
• DOI: 10.1073/pnas.0308527100
• Primary Citation of Related Structures:  
  1RZ8, 1RZ7, 1RZK, 1RZJ, 1RZI, 1RZG, 1RZF


• PubMed Abstract: 
  

The conserved surface of the HIV-1 gp120 envelope glycoprotein that binds to the HIV-1 coreceptor is protected from humoral recognition by multiple layers of camouflage. Here we present sequence and genomic analyses for 12 antibodies that pierce these defenses and determine the crystal structures of 5. The data reveal mechanisms and atomic-level details for three unusual immune features: posttranslational mimicry of coreceptor by tyrosine sulfation of antibody, an alternative molecular mechanism controlling such sulfation, and highly selective V(H)-gene usage. When confronted by extraordinary viral defenses, the immune system unveils novel adaptive capabilities, with tyrosine sulfation enhancing the vocabulary of antigen recognition.

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Organizational Affiliation: 

Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 412d light chain	A, C	231	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 412d heavy chain	B, D	214	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	E, F, G, H, I, J, K	2		N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ASP	D	ASPARTIC ACID C4 H7 N O4 CKLJMWTZIZZHCS-REOHCLBHSA-N
CYS	D	CYSTEINE C3 H7 N O2 S XUJNEKJLAYXESH-REOHCLBHSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYS	A,C	L-PEPTIDE LINKING	C9 H11 N O6 S		TYR

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	E, F, G, H, I, J, K	sucrose	Oligosaccharide /  Nutrient		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.251 
• R-Value Work: 0.201 
• R-Value Observed: 0.201 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.088	α = 90
b = 89.313	β = 110.31
c = 85.863	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-12-24 
• Released Date: 2004-02-03 
Deposition Author(s): Huang, C.C., Venturi, M., Majeed, S., Moore, M.J., Phogat, S., Zhang, M.-Y., Dimitrov, D.S., Hendrickson, W.A., Robinson, J., Sodroski, J., Wyatt, R., Choe, H., Farzan, M., Kwong, P.D.

Revision History 

• Version 1.0: 2004-02-03
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary